Pierrick Roger
| Snapshot Date: 2025-03-20 13:00 -0400 (Thu, 20 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-24 12:04 -0400 (Mon, 24 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4521 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4448 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4414 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2025-03-20 20:12:14 -0400 (Thu, 20 Mar 2025) |
| EndedAt: 2025-03-20 20:14:07 -0400 (Thu, 20 Mar 2025) |
| EllapsedTime: 113.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-20 20:12:54.911][biodb::testContext]
biodb.INFO [2025-03-20 20:12:54.913][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:12:54.915][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-20 20:12:54.916][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:12:54.917][biodb::testContext]
biodb.INFO [2025-03-20 20:12:54.923][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:12:54.926][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 20:12:54.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:12:54.934][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 20:12:54.935][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 20:12:54.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.939][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 20:12:54.960][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 20:12:54.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.963][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 20:12:54.964][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 20:12:54.966][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 20:12:54.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.969][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 20:12:54.970][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 20:12:54.971][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 20:12:54.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.975][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 20:12:54.976][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 20:12:54.977][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 20:12:54.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.981][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 20:12:54.983][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 20:12:54.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.985][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 20:12:54.986][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 20:12:54.987][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 20:12:54.988][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 20:12:54.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.992][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 20:12:54.993][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 20:12:54.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:54.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:54.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:54.997][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 20:12:54.998][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 20:12:54.999][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 20:12:55.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.003][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:12:55.004][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 20:12:55.005][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 20:12:55.006][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 20:12:55.007][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 20:12:55.009][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 20:12:55.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.012][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 20:12:55.013][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 20:12:55.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.017][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 20:12:55.018][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 20:12:55.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.022][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 20:12:55.023][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 20:12:55.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.027][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 20:12:55.028][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 20:12:55.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.032][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 20:12:55.033][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 20:12:55.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.037][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:12:55.038][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 20:12:55.042][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 20:12:55.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.045][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 20:12:55.046][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 20:12:55.047][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 20:12:55.048][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 20:12:55.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.056][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 20:12:55.094][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.119][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 20:12:55.121][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.122][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:12:55.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.126][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:12:55.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:12:55.128][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.129][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 20:12:55.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:12:55.131][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.132][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.133][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:12:55.133][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:12:55.133][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:12:55.133][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:12:55.133][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:12:55.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:12:55.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:12:55.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.140][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:12:55.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:12:55.143][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.143][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.144][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 20:12:55.146][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.147][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:12:55.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.149][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:12:55.150][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.151][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.152][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.153][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.153][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:12:55.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:12:55.155][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.156][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 20:12:55.157][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:12:55.158][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.159][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.160][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:12:55.160][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:12:55.160][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:12:55.160][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:12:55.160][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:12:55.161][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:12:55.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:12:55.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.167][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.168][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:12:55.169][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:12:55.169][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.170][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.171][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 20:12:55.173][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.174][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 20:12:55.175][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:12:55.177][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.178][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.179][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.180][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.181][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:12:55.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:12:55.183][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.184][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 20:12:55.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:12:55.186][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.187][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.188][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.189][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:12:55.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:12:55.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.195][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:12:55.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:12:55.197][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.198][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.208][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 20:12:55.210][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.211][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:12:55.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:12:55.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.218][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:12:55.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:12:55.221][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.222][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 20:12:55.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:12:55.224][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.225][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.226][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:12:55.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:12:55.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.233][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.234][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.235][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:12:55.236][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:12:55.237][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.238][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:12:55.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:12:55.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.247][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 20:12:55.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.249][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 20:12:55.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.256][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 20:12:55.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.258][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 20:12:55.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.261][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 20:12:55.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.270][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 20:12:55.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.290][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 20:12:55.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.294][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 20:12:55.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.310][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 20:12:55.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.312][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 20:12:55.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.319][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 20:12:55.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.321][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 20:12:55.322][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 20:12:55.327][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 20:12:55.329][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 20:12:55.330][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 20:12:55.332][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:12:55.333][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 20:12:55.334][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 20:12:55.336][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 20:12:55.337][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 20:12:55.339][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 20:12:55.340][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:12:55.341][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 20:12:55.343][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 20:12:55.344][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 20:12:55.346][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 20:12:55.347][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 20:12:55.348][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 20:12:55.350][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 20:12:55.351][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:12:55.353][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 20:12:55.354][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 20:12:55.356][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 20:12:55.357][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 20:12:55.359][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 20:12:55.360][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 20:12:55.362][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 20:12:55.363][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 20:12:55.365][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 20:12:55.366][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 20:12:55.368][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 20:12:55.369][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 20:12:55.371][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 20:12:55.372][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 20:12:55.373][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 20:12:55.390][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 20:12:55.392][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 20:12:55.393][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 20:12:55.395][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 20:12:55.396][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 20:12:55.398][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 20:12:55.399][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 20:12:55.401][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 20:12:55.402][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 20:12:55.404][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 20:12:55.406][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 20:12:55.407][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 20:12:55.409][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 20:12:55.410][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 20:12:55.412][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 20:12:55.413][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 20:12:55.415][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 20:12:55.416][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 20:12:55.418][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 20:12:55.419][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 20:12:55.421][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 20:12:55.422][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 20:12:55.424][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 20:12:55.425][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 20:12:55.427][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 20:12:55.428][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 20:12:55.430][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 20:12:55.431][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 20:12:55.433][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 20:12:55.434][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 20:12:55.436][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 20:12:55.437][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 20:12:55.439][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:12:55.440][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:12:55.442][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 20:12:55.443][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 20:12:55.445][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 20:12:55.446][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 20:12:55.448][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 20:12:55.449][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 20:12:55.451][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 20:12:55.452][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 20:12:55.453][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 20:12:55.455][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 20:12:55.456][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 20:12:55.458][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 20:12:55.459][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 20:12:55.461][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 20:12:55.462][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 20:12:55.469][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 20:12:55.471][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:12:55.474][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:12:55.475][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.477][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.486][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 20:12:55.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.488][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 20:12:55.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.492][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 20:12:55.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.509][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 20:12:55.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.515][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 20:12:55.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.539][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 20:12:55.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.541][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 20:12:55.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.546][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 20:12:55.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.558][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 20:12:55.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.562][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 20:12:55.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.564][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 20:12:55.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:12:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:12:55.582][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 20:12:55.591][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 20:12:55.593][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.594][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:12:55.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.599][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.600][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 20:12:55.601][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 20:12:55.602][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:12:55.603][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.604][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 20:12:55.605][self$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 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 20:12:55.605][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 20:12:55.607][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 20:12:55.607][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:12:55.607][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:12:55.607][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:12:55.608][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 20:12:55.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:12:55.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:12:55.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:12:55.614][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:12:55.614][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:12:55.614][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 20:12:55.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:12:55.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:12:55.617][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 20:12:55.618][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 20:12:55.618][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 20:12:55.624][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:12:55.625][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:12:55.627][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 20:12:55.628][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:12:55.630][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:12:55.631][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:12:55.658][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 20:12:55.659][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 20:12:55.663][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 20:12:55.667][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 20:12:55.671][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:12:55.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:12:55.674][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 20:12:55.675][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 20:12:55.683][biodb::testThat]
biodb.INFO [2025-03-20 20:12:55.684][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-20 20:12:55.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:55.686][biodb::testThat]
biodb.TRACE[2025-03-20 20:12:55.690][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-20 20:12:55.691][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:12:55.694][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:12:55.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:12:55.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:55.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:55.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:55.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:55.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:55.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:12:55.727][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.747][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:55.748][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:55.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.774][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:55.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:55.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.779][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:55.780][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:55.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:55.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:55.787][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:55.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:55.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:55.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.794][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.795][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.802][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:55.803][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:55.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.806][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:55.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:55.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.810][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:12:55.811][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.814][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:12:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:55.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:55.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:55.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:55.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.825][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:55.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:55.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:55.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.833][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:12:55.834][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:55.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.837][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:12:55.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:55.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.841][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:55.842][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:55.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.844][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:55.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:55.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:55.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:12:55.928][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-20 20:12:55.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:55.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:55.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:55.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:55.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:55.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:55.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:55.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:55.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.978][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:55.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:55.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:55.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:55.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:55.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:55.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.077][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.080][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.130][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.131][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.133][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.156][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.182][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.183][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.185][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.207][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.208][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.248][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.252][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.259][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.260][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.273][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.277][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.281][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.284][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.285][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.288][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.311][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.312][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.313][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.325][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.335][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.342][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.346][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.370][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.372][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.398][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.399][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.401][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.412][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.413][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.419][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.420][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.426][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.427][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.434][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.435][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.441][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.442][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.455][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.463][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.469][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.476][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.477][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.483][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.484][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.486][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 20:12:56.493][biodb::testThat]
biodb.INFO [2025-03-20 20:12:56.494][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-20 20:12:56.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:56.496][biodb::testThat]
biodb.DEBUG[2025-03-20 20:12:56.509][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-20 20:12:56.516][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:12:56.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-20 20:12:56.521][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:12:56.523][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-20 20:12:56.524][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:12:56.551][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:12:56.553][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:12:56.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:12:56.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:12:56.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:12:56.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:12:56.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:12:56.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:12:56.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:12:56.565][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.590][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:12:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:12:56.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.599][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.603][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:12:56.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:12:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:56.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:56.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.615][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.616][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:56.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.623][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.624][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.627][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:12:56.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.631][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:12:56.632][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.635][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:12:56.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:56.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.638][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.639][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:56.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.646][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.654][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:12:56.655][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:12:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:12:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.662][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.663][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:12:56.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:12:56.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:12:56.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:12:56.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:12:56.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:12:56.707][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-20 20:12:56.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-20 20:12:56.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-20 20:12:56.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-20 20:12:56.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-20 20:12:56.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-20 20:12:56.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-20 20:12:56.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:12:56.725][biodb::testThat]
biodb.INFO [2025-03-20 20:12:56.726][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-20 20:12:56.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:56.728][biodb::testThat]
biodb.TRACE[2025-03-20 20:12:56.731][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.732][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.734][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:12:56.735][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-20 20:12:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:56.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:56.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:56.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:56.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:12:56.780][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-20 20:12:56.784][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 20:12:56.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:12:56.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 20:12:56.820][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:12:56.821][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 20:12:56.843][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 20:12:56.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:12:56.847][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:12:56.848][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:12:57.347][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:12:57.987][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:12:57.992][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 20:12:58.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 20:12:58.031][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-20 20:12:58.048][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:58.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:12:58.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.053][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.055][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.057][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 20:12:58.061][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.062][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-20 20:12:58.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:58.064][biodb::testThat]
biodb.TRACE[2025-03-20 20:12:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:58.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:58.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:58.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:58.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:12:58.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:12:58.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:12:58.152][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:12:58.155][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:12:58.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 20:12:58.157][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:12:58.159][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-20 20:12:58.173][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.174][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-20 20:12:58.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:58.184][biodb::testThat]
biodb.TRACE[2025-03-20 20:12:58.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:58.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:58.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:58.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:58.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:58.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:58.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:12:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:12:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:12:58.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:12:58.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.282][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-20 20:12:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:58.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-20 20:12:58.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:12:58.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:58.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-20 20:12:58.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:12:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:12:58.304][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.305][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-20 20:12:58.306][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:58.307][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.315][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.316][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-20 20:12:58.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:58.318][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.326][biodb::testThat]
biodb.INFO [2025-03-20 20:12:58.326][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-20 20:12:58.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:58.328][biodb::testThat]
biodb.DEBUG[2025-03-20 20:12:58.332][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-20 20:12:58.794][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-20 20:12:59.765][biodb::testThat]
biodb.INFO [2025-03-20 20:12:59.767][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-20 20:12:59.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:12:59.771][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:00.135][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 20:13:00.514][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:00.517][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:00.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.546][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:00.547][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:00.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.549][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:00.551][biodb::testThat]
biodb.INFO [2025-03-20 20:13:00.552][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-20 20:13:00.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:00.554][biodb::testThat]
biodb.TRACE[2025-03-20 20:13:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:00.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:00.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:00.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:00.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:00.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:00.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:00.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:00.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 20:13:00.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:00.662][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 20:13:00.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:00.732][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:00.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 20:13:00.735][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:00.736][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-20 20:13:00.748][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 20:13:00.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 20:13:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:00.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:00.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:00.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:00.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:00.783][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:00.784][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 20:13:00.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:00.787][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 20:13:00.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:00.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:00.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:00.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:00.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:00.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:00.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:00.798][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-20 20:13:00.841][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:00.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-20 20:13:00.844][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:00.845][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:00.846][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:00.847][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:00.848][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:00.849][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:00.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:00.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:00.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:00.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:00.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:00.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:00.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:00.861][scheduler$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 20:13:00.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:00.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:00.896][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-20 20:13:01.231][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-20 20:13:01.810][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:01.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-20 20:13:01.819][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-20 20:13:01.824][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-20 20:13:01.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:01.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:01.832][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:01.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:01.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:01.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:01.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:01.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:01.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:01.852][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 20:13:01.856][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.869][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:01.871][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:01.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.876][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:01.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:01.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.882][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:01.883][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:01.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:01.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.891][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:01.892][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:01.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:01.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:01.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.899][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:01.900][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:01.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:01.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:01.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.908][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:01.909][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:01.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.912][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:01.913][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:01.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.916][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:01.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:01.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.920][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:01.921][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:01.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:01.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.929][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:01.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:01.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:01.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:01.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.937][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:01.938][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:01.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.940][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:01.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:01.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.946][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:01.947][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:01.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:01.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:01.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:01.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:01.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:01.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:01.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:01.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:02.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:02.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:02.005][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-20 20:13:02.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:02.030][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:02.034][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:02.035][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 20:13:02.037][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:02.038][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 20:13:02.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:02.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:02.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:02.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:02.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:02.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:02.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:02.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:02.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:02.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:02.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:02.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:02.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:02.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:02.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:02.107][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-20 20:13:02.108][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:02.110][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-20 20:13:02.111][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:02.113][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:02.114][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:02.115][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:02.116][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:02.117][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:02.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:02.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:02.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:02.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:02.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:02.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:02.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:02.145][scheduler$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 20:13:02.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:02.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:02.151][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-20 20:13:02.483][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-20 20:13:02.817][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:02.821][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-20 20:13:02.829][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-20 20:13:02.835][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-20 20:13:02.838][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:02.841][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:02.843][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:02.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:02.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:02.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:02.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:02.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:02.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:02.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:02.870][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:02.872][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:02.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:02.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.882][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:02.884][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:02.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:02.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:02.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.893][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:02.894][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:02.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:02.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:02.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.921][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:02.922][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:02.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:02.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:02.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.930][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:02.931][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:02.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:02.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.939][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:02.940][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:02.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.943][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:02.944][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.947][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:02.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:02.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.951][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:02.952][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:02.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:02.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:02.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:02.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:02.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:02.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:02.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.968][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:02.969][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:02.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.971][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.972][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:02.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:02.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.976][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:02.977][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:02.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:02.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:02.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:02.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:02.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:02.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:02.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:02.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:03.020][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-20 20:13:03.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:03.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:03.051][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:03.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 20:13:03.054][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:03.055][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 20:13:03.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:03.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:03.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:03.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:03.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:03.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:03.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:03.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:03.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:03.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:03.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:03.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:03.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:03.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:03.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:03.094][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-20 20:13:03.095][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:03.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-20 20:13:03.097][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:03.098][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:03.100][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:03.101][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:03.102][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:03.102][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:03.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:03.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:03.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:03.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:03.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:03.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:03.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:03.115][scheduler$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 20:13:03.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:03.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:03.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-20 20:13:03.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-20 20:13:03.786][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:03.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-20 20:13:03.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-20 20:13:03.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-20 20:13:03.802][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:03.804][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:03.806][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:03.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:03.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:03.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:03.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:03.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:03.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:03.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:03.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.830][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.841][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:03.842][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:03.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.847][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:03.849][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:03.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.854][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:03.856][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:03.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.861][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:03.862][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:03.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.867][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:03.869][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:03.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.874][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:03.876][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:03.882][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:03.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.887][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:03.889][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:03.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.892][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:03.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:03.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.899][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:03.900][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:03.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.903][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:03.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.907][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:03.908][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:03.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:03.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:03.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:03.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:03.952][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-20 20:13:03.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:03.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:03.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:03.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:03.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:03.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:03.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:03.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:03.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:03.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:03.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:03.995][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-20 20:13:03.996][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:03.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-20 20:13:03.999][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:04.001][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:04.002][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:04.003][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:04.004][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:04.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:04.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:04.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:04.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:04.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:04.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:04.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:04.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:04.019][scheduler$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 20:13:04.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:04.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:04.024][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-20 20:13:04.359][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-20 20:13:04.694][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:04.698][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-20 20:13:04.704][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-20 20:13:04.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-20 20:13:04.712][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:04.714][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:04.716][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:04.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:04.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:04.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:04.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:04.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:04.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:04.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:04.741][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.754][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:04.755][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:04.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.760][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:04.761][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:04.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.765][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:04.767][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:04.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:04.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:04.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.774][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:04.776][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:04.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.779][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:04.781][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.784][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:04.785][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:04.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.788][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:04.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:04.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.791][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:04.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:04.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.797][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:04.798][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:04.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:04.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:04.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.806][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:04.807][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:04.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:04.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:04.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:04.854][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-20 20:13:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:04.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:04.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:04.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:04.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:04.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:04.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:04.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:04.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:04.889][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-20 20:13:04.890][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:04.892][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-20 20:13:04.893][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:04.894][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:04.895][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:04.896][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:04.897][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:04.898][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:04.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:04.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:04.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:04.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:04.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:04.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:04.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:04.910][scheduler$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 20:13:04.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:04.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:04.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-20 20:13:05.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-20 20:13:05.579][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:05.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-20 20:13:05.585][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-20 20:13:05.587][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-20 20:13:05.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:05.596][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:05.598][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:05.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:05.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:05.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:05.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:05.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:05.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:05.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:05.615][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.617][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.624][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:05.625][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:05.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.627][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.629][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:05.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:05.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.633][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:05.634][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:05.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.638][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:05.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:05.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.641][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.642][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:05.643][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:05.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.646][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:05.647][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.650][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:05.652][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:05.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.655][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:05.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:05.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.664][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:05.665][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:05.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.672][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:05.673][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:05.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:05.736][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-20 20:13:05.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:05.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:05.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:05.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:05.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:05.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:05.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:05.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:05.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:05.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:05.768][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-20 20:13:05.769][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:05.770][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-20 20:13:05.772][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:05.773][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:05.774][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:05.775][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:05.776][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:05.777][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:05.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:05.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:05.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:05.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:05.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:05.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:05.790][scheduler$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 20:13:05.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:05.794][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:05.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-20 20:13:06.127][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-20 20:13:06.476][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:06.480][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-20 20:13:06.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-20 20:13:06.493][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-20 20:13:06.496][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:06.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:06.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:06.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:06.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:06.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:06.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:06.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:06.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:06.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:06.528][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.541][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:06.543][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:06.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.547][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:06.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:06.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:06.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.561][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:06.563][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:06.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:06.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:06.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:06.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:06.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:06.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:06.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.577][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:06.578][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:06.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.581][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:06.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.585][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:06.586][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.587][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.589][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:06.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.592][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:06.593][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:06.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:06.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:06.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.600][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:06.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:06.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:06.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:06.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.616][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:06.617][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:06.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:06.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:06.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:06.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:06.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:06.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:06.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:06.668][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-20 20:13:06.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:06.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:06.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:06.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:06.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:06.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:06.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:06.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:06.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:06.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:06.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:06.689][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-20 20:13:06.690][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:06.692][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-20 20:13:06.693][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:06.694][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:06.695][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:06.696][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:06.697][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:06.697][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:06.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:06.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:06.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:06.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:06.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:06.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:06.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:06.710][scheduler$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 20:13:06.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:06.713][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:06.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-20 20:13:07.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-20 20:13:07.391][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:07.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-20 20:13:07.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-20 20:13:07.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-20 20:13:07.411][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:07.414][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:07.416][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:07.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:07.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:07.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:07.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:07.434][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 20:13:07.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:07.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:07.441][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.443][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.453][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:07.455][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:07.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.459][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:07.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:07.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.464][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:07.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:07.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:07.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:07.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:07.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:07.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:07.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:07.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:07.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:07.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:07.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:07.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:07.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.501][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:07.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.505][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:07.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:07.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:07.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:07.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:07.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:07.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.520][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:07.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:07.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:07.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:07.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.528][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:07.529][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:07.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.531][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.535][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:07.536][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:07.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.539][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:07.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:07.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:07.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:07.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:07.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:07.579][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-20 20:13:07.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:07.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:07.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:07.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:07.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:07.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:07.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:07.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:07.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:07.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:07.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:07.601][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-20 20:13:07.602][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:07.603][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-20 20:13:07.604][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:07.605][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:07.606][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:07.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:07.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:07.609][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:07.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:07.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:07.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:07.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:07.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:07.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:07.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:07.622][scheduler$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 20:13:07.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:07.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:07.626][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-20 20:13:07.961][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-20 20:13:08.303][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:08.307][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-20 20:13:08.315][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-20 20:13:08.320][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-20 20:13:08.323][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:08.326][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:08.329][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:08.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:08.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:08.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:08.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:08.348][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 20:13:08.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:08.351][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 20:13:08.366][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.367][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.376][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:08.377][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:08.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.386][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:08.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:08.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:08.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:08.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:08.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:08.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:08.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:08.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.402][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:08.403][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:08.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:08.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:08.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:08.411][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:08.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.414][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:08.415][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.417][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:08.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.422][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:08.423][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:08.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:08.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:08.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.430][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:08.431][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:08.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:08.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.439][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:08.440][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:08.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.441][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.443][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:08.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.446][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:08.447][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:08.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:08.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:08.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:08.493][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-20 20:13:08.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:08.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:08.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:08.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:08.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:08.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:08.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:08.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:08.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:08.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:08.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:08.515][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-20 20:13:08.516][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:08.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-20 20:13:08.518][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:08.519][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:08.520][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:08.521][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:08.522][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:08.523][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:08.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:08.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:08.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:08.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:08.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:08.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:08.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:08.540][scheduler$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 20:13:08.543][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:08.544][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:08.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-20 20:13:08.885][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-20 20:13:09.226][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:09.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-20 20:13:09.232][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-20 20:13:09.235][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-20 20:13:09.236][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:09.238][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:09.239][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:09.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:09.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:09.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:09.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:09.249][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 20:13:09.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:09.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:09.253][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.254][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.256][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.262][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:09.263][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:09.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.266][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:09.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:09.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.271][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:09.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:09.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:09.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:09.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:09.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:09.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:09.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:09.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:09.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:09.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.296][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:09.297][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:09.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.300][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:09.301][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.305][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:09.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:09.310][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:09.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:09.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.317][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:09.318][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:09.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:09.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:09.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.326][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:09.327][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:09.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.334][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:09.335][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:09.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.338][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:09.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:09.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:09.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:09.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:09.383][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-20 20:13:09.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:09.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:09.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:09.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:09.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:09.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:09.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:09.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:09.420][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-20 20:13:09.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:09.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-20 20:13:09.424][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:09.426][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:09.427][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:09.428][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:09.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:09.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:09.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:09.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:09.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:09.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:09.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:09.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:09.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:09.444][scheduler$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 20:13:09.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:09.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:09.449][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-20 20:13:09.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-20 20:13:10.125][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:10.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-20 20:13:10.137][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-20 20:13:10.142][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-20 20:13:10.145][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:10.148][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:10.151][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:10.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:10.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:10.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:10.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:10.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:10.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:10.173][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 20:13:10.177][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.179][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.189][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:10.191][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:10.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.195][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:10.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:10.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.200][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:10.201][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:10.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.209][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:10.210][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:10.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:10.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:10.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.217][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:10.218][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:10.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:10.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.224][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:10.225][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:10.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.228][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:10.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:10.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.236][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:10.237][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:10.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.239][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:10.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:10.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.244][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:10.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:10.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.251][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:10.252][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:10.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:10.260][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:10.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:10.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:10.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:10.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:10.314][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-20 20:13:10.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:10.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:10.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:10.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:10.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:10.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:10.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:10.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:10.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:10.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:10.336][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-20 20:13:10.336][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:10.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-20 20:13:10.339][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:10.340][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:10.341][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:10.342][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:10.343][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:10.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:10.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:10.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:10.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:10.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:10.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:10.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:10.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:10.357][scheduler$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 20:13:10.359][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:10.360][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:10.362][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-20 20:13:10.695][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-20 20:13:11.038][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:11.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-20 20:13:11.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-20 20:13:11.058][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-20 20:13:11.061][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:11.064][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:11.067][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:11.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:11.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:11.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:11.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:11.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:11.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:11.090][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.TRACE[2025-03-20 20:13:11.094][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.096][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.107][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:11.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:11.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:11.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.117][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:11.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:11.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:11.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.126][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:11.135][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:11.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:11.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:11.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.146][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:11.147][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:11.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:11.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:11.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.155][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:11.156][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:11.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.159][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:11.161][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.163][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.164][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:11.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.168][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:11.169][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:11.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.171][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:11.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:11.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.177][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:11.178][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:11.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:11.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:11.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.239][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:11.241][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:11.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.244][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:11.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:11.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.248][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:11.249][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:11.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:11.296][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-20 20:13:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:11.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:11.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:11.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:11.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:11.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:11.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:11.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:11.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:11.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:11.319][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-20 20:13:11.320][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:11.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-20 20:13:11.323][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:11.324][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:11.325][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:11.326][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:11.327][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:11.328][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:11.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:11.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:11.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:11.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:11.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:11.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:11.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:11.341][scheduler$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 20:13:11.344][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:11.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:11.347][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-20 20:13:11.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-20 20:13:12.017][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:12.022][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-20 20:13:12.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-20 20:13:12.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-20 20:13:12.037][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:12.040][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:12.042][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:12.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:12.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:12.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:12.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:12.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:12.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:12.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:12.066][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.078][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:12.080][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:12.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:12.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.089][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:12.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:12.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:12.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:12.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.098][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:12.099][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:12.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:12.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:12.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.106][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:12.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:12.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.123][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:12.124][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:12.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.128][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:12.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:12.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:12.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:12.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:12.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:12.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.144][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:12.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:12.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.147][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:12.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:12.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:12.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:12.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:12.161][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:12.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:12.205][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-20 20:13:12.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:12.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:12.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:12.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:12.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:12.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:12.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:12.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:12.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:12.231][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-20 20:13:12.232][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:12.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-20 20:13:12.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:12.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:12.237][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:12.238][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:12.239][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:12.240][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:12.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:12.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:12.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:12.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:12.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:12.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:12.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:12.252][scheduler$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 20:13:12.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:12.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:12.258][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-20 20:13:12.596][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-20 20:13:12.936][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:12.939][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-20 20:13:12.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-20 20:13:12.947][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-20 20:13:12.949][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:12.951][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:12.953][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:12.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:12.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:12.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:12.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:12.965][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 20:13:12.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:12.968][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 20:13:12.971][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:12.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:12.995][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:12.997][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:12.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:12.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:13.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.004][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:13.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:13.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.014][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:13.015][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:13.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.017][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.018][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:13.019][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:13.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:13.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:13.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.026][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.027][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:13.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.036][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.037][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.045][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:13.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:13.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:13.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.053][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:13.054][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:13.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.057][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:13.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:13.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.062][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:13.063][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:13.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:13.107][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-20 20:13:13.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:13.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:13.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:13.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:13.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:13.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:13.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:13.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:13.131][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-20 20:13:13.132][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:13.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-20 20:13:13.135][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:13.137][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:13.138][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:13.139][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:13.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:13.141][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:13.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:13.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:13.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:13.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:13.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:13.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:13.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:13.155][scheduler$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 20:13:13.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:13.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:13.160][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-20 20:13:13.501][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-20 20:13:13.838][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:13.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-20 20:13:13.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-20 20:13:13.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-20 20:13:13.860][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:13.863][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:13.875][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:13.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:13.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:13.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:13.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:13.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:13.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:13.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, 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 20:13:13.905][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.907][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.916][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:13.917][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:13.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.920][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:13.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:13.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.926][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:13.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:13.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:13.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.934][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:13.935][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:13.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.939][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:13.940][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:13.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.941][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.943][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:13.944][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:13.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.947][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:13.948][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.950][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.951][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:13.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:13.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.956][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.957][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.959][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:13.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.964][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:13.965][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:13.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.973][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:13.974][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:13.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.976][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.977][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:13.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:13.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.981][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:13.982][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:13.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.984][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:13.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:13.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:13.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:13.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:14.026][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-20 20:13:14.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:14.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:14.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:14.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:14.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:14.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:14.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:14.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:14.050][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-20 20:13:14.052][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:14.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-20 20:13:14.055][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:14.056][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:14.057][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:14.058][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:14.059][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:14.060][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:14.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:14.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:14.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:14.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:14.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:14.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:14.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:14.081][scheduler$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 20:13:14.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:14.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:14.086][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-20 20:13:14.417][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-20 20:13:14.758][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:14.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-20 20:13:14.770][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-20 20:13:14.776][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-20 20:13:14.780][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:14.783][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:14.785][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:14.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:14.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:14.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:14.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:14.804][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 20:13:14.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:14.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:14.812][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.814][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.824][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:14.826][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:14.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.835][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:14.836][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:14.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:14.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:14.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.844][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:14.846][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:14.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:14.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:14.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.853][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:14.854][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:14.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.861][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:14.863][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:14.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.866][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:14.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.870][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:14.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.874][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:14.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:14.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.882][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:14.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:14.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.891][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:14.892][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:14.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.895][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.899][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:14.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:14.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:14.947][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-20 20:13:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:14.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:14.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:14.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:14.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:14.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:14.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:14.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:14.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:14.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:14.984][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-20 20:13:14.985][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:14.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-20 20:13:14.988][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:14.989][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:14.990][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:14.991][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:14.992][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:14.993][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:14.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:14.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:14.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:15.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:15.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:15.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:15.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:15.007][scheduler$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 20:13:15.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:15.011][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:15.013][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-20 20:13:15.346][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-20 20:13:15.687][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:15.692][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-20 20:13:15.699][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-20 20:13:15.705][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-20 20:13:15.708][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:15.710][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:15.713][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:15.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:15.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:15.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:15.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:15.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:15.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:15.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:15.739][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.741][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.752][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:15.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:15.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.763][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:15.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:15.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.766][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:15.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:15.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.772][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:15.773][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:15.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:15.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:15.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:15.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:15.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.790][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:15.791][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:15.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.794][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:15.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:15.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:15.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:15.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.812][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:15.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:15.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.815][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:15.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:15.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.821][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:15.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:15.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:15.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:15.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.830][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:15.831][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:15.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.835][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:15.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:15.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:15.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:15.895][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-20 20:13:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:15.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:15.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:15.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:15.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:15.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:15.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:15.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:15.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:15.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:15.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:15.917][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-20 20:13:15.918][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:15.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-20 20:13:15.920][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:15.921][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:15.922][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:15.923][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:15.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:15.925][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:15.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:15.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:15.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:15.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:15.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:15.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:15.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:15.938][scheduler$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 20:13:15.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:15.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:15.943][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-20 20:13:16.274][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-20 20:13:16.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:16.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-20 20:13:16.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-20 20:13:16.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-20 20:13:16.621][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:16.622][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:16.624][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:16.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:16.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:16.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:16.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:16.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:16.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:16.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:16.636][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.639][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.644][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:16.645][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:16.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.648][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:16.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:16.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.652][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:16.652][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:16.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:16.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:16.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.659][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:16.660][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:16.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.662][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:16.668][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:16.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.670][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.675][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:16.676][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:16.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.678][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.679][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:16.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.682][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.683][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:16.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:16.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:16.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:16.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:16.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.695][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:16.696][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:16.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:16.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.703][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:16.704][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:16.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.733][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:16.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:16.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:16.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.748][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.750][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:16.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:16.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:16.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:16.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:16.795][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-20 20:13:16.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:16.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:16.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:16.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:16.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:16.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:16.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:16.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:16.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:16.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:16.820][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-20 20:13:16.821][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:16.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-20 20:13:16.824][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:16.825][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:16.826][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:16.827][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:16.828][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:16.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:16.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:16.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:16.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:16.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:16.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:16.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:16.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:16.844][scheduler$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 20:13:16.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:16.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:16.850][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-20 20:13:17.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-20 20:13:17.524][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:17.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-20 20:13:17.537][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-20 20:13:17.543][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-20 20:13:17.546][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:17.549][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:17.552][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:17.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:17.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:17.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:17.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:17.572][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 20:13:17.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:17.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, 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 20:13:17.579][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.591][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:17.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:17.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.597][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.602][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:17.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:17.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:17.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.611][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:17.612][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:17.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.614][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:17.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:17.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.619][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:17.620][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:17.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:17.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.627][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:17.636][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:17.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.638][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.639][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:17.640][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:17.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.647][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:17.648][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:17.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:17.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:17.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.654][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:17.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:17.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:17.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:17.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.662][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:17.663][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:17.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.666][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:17.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.670][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:17.671][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:17.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:17.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:17.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:17.714][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-20 20:13:17.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:17.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:17.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:17.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:17.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:17.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:17.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:17.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:17.735][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-20 20:13:17.736][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:17.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-20 20:13:17.739][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:17.740][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:17.741][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:17.741][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:17.742][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:17.743][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:17.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:17.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:17.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:17.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:17.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:17.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:17.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:17.755][scheduler$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 20:13:17.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:17.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:17.760][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-20 20:13:18.092][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-20 20:13:18.432][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:18.435][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-20 20:13:18.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-20 20:13:18.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-20 20:13:18.445][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:18.446][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:18.447][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:18.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:18.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:18.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:18.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:18.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:18.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:18.459][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 20:13:18.462][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.471][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:18.485][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:18.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:18.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.493][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:18.494][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:18.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.498][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:18.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:18.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:18.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:18.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.510][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:18.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:18.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:18.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:18.520][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:18.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.523][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:18.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.526][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:18.532][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:18.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:18.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.540][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:18.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:18.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:18.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:18.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.548][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:18.549][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:18.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.556][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:18.557][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:18.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.560][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:18.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:18.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:18.605][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-20 20:13:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:18.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:18.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:18.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:18.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:18.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:18.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:18.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:18.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:18.629][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-20 20:13:18.630][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:18.632][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-20 20:13:18.633][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:18.635][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:18.636][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:18.637][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:18.638][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:18.639][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:18.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:18.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:18.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:18.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:18.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:18.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:18.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:18.653][scheduler$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 20:13:18.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:18.658][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:18.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-20 20:13:18.989][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-20 20:13:19.332][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-20 20:13:19.336][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-20 20:13:19.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-20 20:13:19.345][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-20 20:13:19.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-20 20:13:19.353][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:19.355][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:19.357][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:19.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:19.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:19.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:19.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:19.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:19.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:19.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:19.381][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.383][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.393][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:19.394][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:19.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:19.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.402][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:19.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:19.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:19.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:19.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:19.412][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:19.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:19.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:19.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.419][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:19.420][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:19.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:19.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:19.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.427][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:19.428][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:19.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.431][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:19.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.438][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:19.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:19.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.441][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:19.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:19.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.446][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:19.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:19.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:19.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:19.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:19.455][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:19.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.458][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:19.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:19.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:19.462][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:19.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:19.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:19.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:19.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:19.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:19.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:19.506][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-20 20:13:19.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:19.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:19.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:19.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:19.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:19.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:19.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:19.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:19.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:19.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:19.533][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 20:13:19.534][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-20 20:13:19.535][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:19.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-20 20:13:19.538][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:19.539][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:19.540][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:19.541][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:19.542][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:19.543][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:19.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:19.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:19.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:19.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:19.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:19.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:19.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:19.555][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-20 20:13:19.557][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:19.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:19.560][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-20 20:13:19.891][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 20:13:20.226][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:20.230][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-20 20:13:20.236][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-20 20:13:20.241][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-20 20:13:20.244][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:20.246][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:20.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:20.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:20.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:20.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:20.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:20.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:20.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:20.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:20.271][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.273][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.276][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.284][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:20.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:20.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.289][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:20.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:20.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.294][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:20.295][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:20.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:20.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:20.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.304][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:20.305][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:20.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:20.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:20.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:20.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:20.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:20.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:20.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.320][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:20.321][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:20.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.323][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.324][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:20.326][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:20.334][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:20.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:20.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:20.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.341][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:20.342][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:20.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:20.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:20.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.350][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:20.351][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:20.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.354][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:20.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:20.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:20.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:20.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:20.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:20.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:20.419][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-20 20:13:20.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:20.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:20.451][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 20:13:20.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:20.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:20.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:20.861][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:21.272][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:21.275][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 20:13:21.280][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 20:13:21.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:21.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:21.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:21.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:21.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:21.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:21.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:21.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:21.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:21.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:21.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:21.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:21.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-03-20 20:13:21.823][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-20 20:13:21.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:21.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:21.828][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:22.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:22.498][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:22.503][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-20 20:13:22.511][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-20 20:13:22.520][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:22.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:22.529][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:22.534][private$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 20:13:22.871][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 20:13:23.208][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:23.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-20 20:13:23.223][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-20 20:13:23.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:23.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:23.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:23.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:23.247][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 20:13:23.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:23.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:23.254][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-20 20:13:23.256][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:23.259][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-20 20:13:23.261][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:23.263][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:23.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:23.267][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:23.268][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:23.270][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:23.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:23.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:23.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:23.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:23.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:23.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:23.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:23.287][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-20 20:13:23.290][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:23.291][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:23.293][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-20 20:13:23.626][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 20:13:23.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:23.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-20 20:13:23.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-20 20:13:24.068][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-20 20:13:24.075][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:24.086][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:24.088][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:24.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:24.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:24.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:24.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:24.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:24.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:24.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:24.104][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.105][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.112][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:24.113][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:24.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:24.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.121][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:24.122][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:24.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:24.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:24.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.137][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:24.139][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:24.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:24.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.149][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:24.150][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:24.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.152][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:24.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.159][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:24.160][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:24.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.164][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:24.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:24.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.168][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:24.169][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:24.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.179][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.187][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:24.188][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:24.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:24.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:24.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.197][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:24.198][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:24.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.202][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:24.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.207][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:24.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:24.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.209][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:24.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:24.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:24.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:24.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:24.273][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-20 20:13:24.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:24.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:24.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:24.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:24.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:24.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:24.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:24.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:24.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:24.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:24.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:24.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:24.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:24.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:24.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:24.337][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 20:13:24.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:24.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:24.340][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-20 20:13:24.341][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:24.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-20 20:13:24.345][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:24.346][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:24.347][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:24.348][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:24.350][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:24.351][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:24.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:24.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:24.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:24.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:24.363][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 20:13:24.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:24.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:24.366][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-20 20:13:24.370][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:24.371][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:24.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-20 20:13:24.738][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-20 20:13:25.104][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:25.106][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-20 20:13:25.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-20 20:13:25.112][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-20 20:13:25.113][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:25.114][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:25.115][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:25.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:25.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:25.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:25.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:25.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:25.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:25.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:25.128][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.136][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:25.137][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:25.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.140][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:25.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:25.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.143][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:25.144][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:25.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:25.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:25.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.151][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:25.152][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:25.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:25.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:25.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.159][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:25.160][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:25.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:25.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.167][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:25.168][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:25.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.169][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.171][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:25.172][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:25.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:25.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.178][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.179][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.186][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:25.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:25.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:25.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.194][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:25.195][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:25.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:25.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.202][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:25.202][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:25.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.204][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:25.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:25.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:25.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:25.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:25.259][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-20 20:13:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:25.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:25.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:25.287][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 20:13:25.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:25.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:25.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:25.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:26.105][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:26.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-20 20:13:26.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-20 20:13:26.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:26.710][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:26.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-20 20:13:26.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:26.715][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-20 20:13:26.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:26.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:26.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:26.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:26.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:26.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:26.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:26.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:26.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:26.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:26.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:27.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.265][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:27.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:27.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:27.278][biodb::testThat]
biodb.INFO [2025-03-20 20:13:27.279][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-20 20:13:27.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:27.281][biodb::testThat]
biodb.TRACE[2025-03-20 20:13:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 20:13:27.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 20:13:27.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:27.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:27.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:27.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:27.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:27.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:27.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:27.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:27.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:27.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:27.322][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:27.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:27.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:27.328][private$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 20:13:27.660][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:27.998][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:28.004][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-20 20:13:28.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-20 20:13:28.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:28.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:28.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:28.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:28.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:28.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:28.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:28.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:28.069][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 20:13:28.074][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:28.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:28.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:28.415][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:28.749][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:28.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-20 20:13:28.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-20 20:13:28.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:28.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:28.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:28.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:28.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:28.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:28.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:28.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:28.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:28.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:28.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:28.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:28.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:28.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:28.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:28.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:28.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:28.866][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:28.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:28.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:28.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:28.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:28.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:28.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:28.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:28.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.887][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.888][private$selectFields]
biodb.TRACE[2025-03-20 20:13:28.889][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:28.890][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:28.891][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.908][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.921][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.923][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.931][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:28.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.960][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 20:13:28.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:28.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:28.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:28.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:28.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:28.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:28.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:28.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.987][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.988][private$selectFields]
biodb.TRACE[2025-03-20 20:13:28.989][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:28.990][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:28.991][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:28.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.993][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:28.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:28.996][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.998][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:28.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.002][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.003][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.004][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.008][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:29.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.023][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:29.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:29.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:29.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:29.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:29.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:29.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:29.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.046][private$selectFields]
biodb.TRACE[2025-03-20 20:13:29.047][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:29.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:29.049][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.055][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.081][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.085][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:29.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.089][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.091][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.092][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:29.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.108][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 20:13:29.109][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:29.110][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:29.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:29.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:29.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:29.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:29.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:29.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:29.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:29.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:29.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:29.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:29.205][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:29.208][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:29.209][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:29.211][private$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 20:13:29.544][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 20:13:29.879][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:29.882][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-20 20:13:29.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-20 20:13:29.894][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 20:13:29.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:29.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:29.904][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:30.239][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:30.578][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:30.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-20 20:13:30.588][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-20 20:13:30.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:30.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:30.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:30.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:30.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:30.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:30.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:30.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:30.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:30.717][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:30.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:30.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:30.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.765][private$selectFields]
biodb.TRACE[2025-03-20 20:13:30.766][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:30.767][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:30.768][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.769][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.774][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.778][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.780][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.783][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:30.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.804][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 20:13:30.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.813][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 20:13:30.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.815][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.TRACE[2025-03-20 20:13:30.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.860][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.861][private$selectFields]
biodb.TRACE[2025-03-20 20:13:30.862][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:30.863][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:30.864][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.865][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.866][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.869][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.870][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.885][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.887][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.889][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.890][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:30.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.904][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:30.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:30.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:30.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:30.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:30.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:30.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:30.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.924][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.925][private$selectFields]
biodb.TRACE[2025-03-20 20:13:30.926][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:30.927][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:30.928][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.929][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.930][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.936][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.939][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:30.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.943][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:30.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.957][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 20:13:30.965][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:30.966][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:30.976][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:30.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:30.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:30.984][biodb::testThat]
biodb.INFO [2025-03-20 20:13:30.985][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-20 20:13:30.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:30.987][biodb::testThat]
biodb.TRACE[2025-03-20 20:13:30.991][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 20:13:30.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 20:13:30.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:30.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:30.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:31.025][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.028][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 20:13:31.031][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.032][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 20:13:31.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.058][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.061][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.062][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 20:13:31.063][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.064][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 20:13:31.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.110][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:31.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.130][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.131][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.132][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.133][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.133][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.134][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.135][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.137][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.145][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.150][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.151][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.156][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.168][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 20:13:31.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.188][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.189][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.190][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.191][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.192][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.193][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.201][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.203][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.206][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.218][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:31.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.238][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.239][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.240][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.241][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.243][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.249][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.250][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.255][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.267][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 20:13:31.268][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:31.269][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:31.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:31.307][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 20:13:31.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.320][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 20:13:31.324][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.327][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 20:13:31.329][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.331][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 20:13:31.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.400][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:31.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.420][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.421][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.422][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.422][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.424][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.425][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.427][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.428][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.432][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.433][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.437][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.450][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 20:13:31.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.469][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.470][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.471][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.479][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.491][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.496][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.510][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:31.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.530][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.531][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.532][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.533][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.538][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.539][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.543][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.544][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.546][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.549][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.562][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 20:13:31.563][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:31.564][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:31.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:31.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:31.581][biodb::testThat]
biodb.INFO [2025-03-20 20:13:31.582][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-20 20:13:31.583][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:31.584][biodb::testThat]
biodb.TRACE[2025-03-20 20:13:31.587][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-20 20:13:31.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-20 20:13:31.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:31.625][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.629][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.630][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-20 20:13:31.632][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.633][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-20 20:13:31.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.659][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.662][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-20 20:13:31.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.673][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-20 20:13:31.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:31.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.722][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:31.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.742][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.743][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.744][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.745][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.746][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.747][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.751][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.752][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.754][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.755][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.760][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.773][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-20 20:13:31.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.793][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.794][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.795][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.798][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.800][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.801][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.804][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.805][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.806][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.807][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.810][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.823][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:31.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.849][private$selectFields]
biodb.TRACE[2025-03-20 20:13:31.850][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:31.851][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:31.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.857][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.860][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:31.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.866][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:31.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:31.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.879][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-20 20:13:31.880][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:31.881][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:31.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:31.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.935][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-20 20:13:31.937][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.938][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-20 20:13:31.941][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:31.944][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:31.946][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-20 20:13:31.947][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:31.948][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-20 20:13:31.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:31.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:31.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:31.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:31.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:31.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:31.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:31.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:31.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:32.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:32.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:32.023][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-20 20:13:32.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:32.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:32.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:32.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.043][private$selectFields]
biodb.TRACE[2025-03-20 20:13:32.044][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:32.045][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:32.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.056][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.060][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:32.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.073][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-20 20:13:32.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:32.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:32.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:32.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.093][private$selectFields]
biodb.TRACE[2025-03-20 20:13:32.094][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:32.095][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:32.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.100][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.101][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.104][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.105][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:32.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.123][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-20 20:13:32.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:32.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:32.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.143][private$selectFields]
biodb.TRACE[2025-03-20 20:13:32.143][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-20 20:13:32.144][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-20 20:13:32.145][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.150][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.151][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.153][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.154][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.155][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-20 20:13:32.156][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.157][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.160][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-20 20:13:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:32.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.172][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-20 20:13:32.173][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-20 20:13:32.174][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-20 20:13:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-20 20:13:32.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:32.208][biodb::testThat]
biodb.INFO [2025-03-20 20:13:32.209][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-20 20:13:32.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:32.211][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:32.212][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-20 20:13:32.214][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:32.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-20 20:13:32.216][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:32.218][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:32.219][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:32.220][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:32.221][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:32.221][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:32.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:32.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:32.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:32.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-20 20:13:32.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:32.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:32.240][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-20 20:13:32.574][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-20 20:13:32.911][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:32.916][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-20 20:13:32.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-20 20:13:32.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-20 20:13:32.932][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:32.935][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:32.938][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:32.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:32.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:32.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:32.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:32.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:32.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:32.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:32.963][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:32.965][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:32.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:32.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:32.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.976][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:32.977][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:32.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.981][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:32.982][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:32.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.985][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.986][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:32.987][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:32.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.991][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:32.992][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:32.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.994][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.995][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:32.996][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:32.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:32.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:32.999][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:33.001][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:33.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.004][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:33.005][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:33.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.007][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:33.008][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:33.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.011][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:33.012][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:33.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:33.016][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:33.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:33.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:33.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:33.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:33.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:33.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:33.067][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-20 20:13:33.067][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-20 20:13:33.075][biodb::testThat]
biodb.INFO [2025-03-20 20:13:33.076][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 20:13:33.076][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:33.077][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:33.085][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-20 20:13:33.086][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-20 20:13:33.087][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-20 20:13:33.089][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-20 20:13:33.090][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-20 20:13:33.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:33.092][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:33.093][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:33.094][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:33.095][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:33.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:33.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:33.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:33.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:33.106][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 20:13:33.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:33.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:33.109][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-20 20:13:33.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:33.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:33.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-20 20:13:33.447][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 20:13:33.784][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:33.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-20 20:13:33.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-20 20:13:33.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:33.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:33.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:33.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:33.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:33.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:33.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:33.822][scheduler$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 20:13:33.828][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:33.830][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:33.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-20 20:13:34.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-20 20:13:34.510][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:34.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-20 20:13:34.516][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-20 20:13:34.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:34.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:34.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:34.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:34.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:34.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:34.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:34.528][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-20 20:13:34.531][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:34.532][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:34.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-20 20:13:34.865][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 20:13:35.204][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:35.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-20 20:13:35.210][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-20 20:13:35.213][private$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 20:13:35.214][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:35.215][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-20 20:13:35.216][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:35.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:35.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:35.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:35.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:35.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:35.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:35.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:35.229][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.230][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.237][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:35.238][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:35.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.242][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:35.243][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:35.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.246][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:35.247][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:35.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.249][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.250][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.251][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.254][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.255][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.258][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:35.259][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:35.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.282][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:35.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:35.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.286][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:35.287][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:35.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.289][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:35.291][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:35.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.293][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:35.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:35.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:35.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:35.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:35.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:35.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:35.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:35.331][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.332][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.339][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:35.340][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:35.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.343][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.347][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:35.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:35.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:35.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:35.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:35.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:35.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:35.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.363][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.363][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.365][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.370][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.371][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.374][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.378][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:35.379][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:35.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.385][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.386][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.393][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:35.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:35.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.396][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:35.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:35.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.401][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:35.402][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:35.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.405][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:35.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.408][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:35.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:35.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:35.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:35.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:35.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:35.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:35.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:35.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:35.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:35.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:35.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-20 20:13:35.461][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.469][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:35.470][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:35.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.477][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:35.478][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:35.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.480][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:35.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:35.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.485][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:35.486][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:35.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.493][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.494][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:35.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.505][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:35.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.509][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:35.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:35.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.512][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:35.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.518][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.524][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:35.525][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:35.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:35.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:35.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.532][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:35.533][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:35.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.536][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:35.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:35.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.539][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:35.540][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:35.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:35.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:35.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:35.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:35.611][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-20 20:13:35.612][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-20 20:13:35.613][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-20 20:13:35.625][biodb::testThat]
biodb.INFO [2025-03-20 20:13:35.626][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-20 20:13:35.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:35.628][biodb::testThat]
biodb.INFO [2025-03-20 20:13:35.649][biodb::testThat]
biodb.INFO [2025-03-20 20:13:35.650][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-20 20:13:35.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:35.652][biodb::testThat]
biodb.INFO [2025-03-20 20:13:35.660][biodb::testThat]
biodb.INFO [2025-03-20 20:13:35.661][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-20 20:13:35.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:35.662][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:35.665][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:35.668][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:35.669][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:35.670][private$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 20:13:36.041][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 20:13:36.490][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:36.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-20 20:13:36.504][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-20 20:13:36.528][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:36.531][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:36.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:36.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:36.537][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:36.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:36.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:36.542][ef$get] fields variable is a list.
biodb.INFO [2025-03-20 20:13:36.544][biodb::testThat]
biodb.INFO [2025-03-20 20:13:36.546][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-20 20:13:36.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:36.549][biodb::testThat]
biodb.ERROR[2025-03-20 20:13:36.566][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-20 20:13:36.584][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-20 20:13:36.597][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 20:13:36.599][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 20:13:36.600][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 20:13:36.601][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 20:13:36.602][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:36.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:36.603][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:36.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:36.605][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 20:13:36.627][biodb::testContext]
biodb.INFO [2025-03-20 20:13:36.628][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:36.629][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-20 20:13:36.630][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:36.631][biodb::testContext]
biodb.INFO [2025-03-20 20:13:36.633][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:36.635][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:36.639][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:36.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 20:13:36.641][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.645][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 20:13:36.646][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.649][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 20:13:36.650][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.654][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 20:13:36.654][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 20:13:36.655][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 20:13:36.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.658][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 20:13:36.659][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 20:13:36.660][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 20:13:36.661][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.664][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 20:13:36.665][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 20:13:36.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.668][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.DEBUG[2025-03-20 20:13:36.669][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 20:13:36.670][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 20:13:36.671][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 20:13:36.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.675][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 20:13:36.676][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.680][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 20:13:36.681][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 20:13:36.682][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 20:13:36.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.686][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:36.686][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 20:13:36.687][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 20:13:36.688][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 20:13:36.689][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 20:13:36.690][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 20:13:36.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.694][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 20:13:36.695][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 20:13:36.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.698][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 20:13:36.699][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 20:13:36.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.702][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 20:13:36.702][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 20:13:36.703][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 20:13:36.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.707][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 20:13:36.708][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 20:13:36.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.711][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 20:13:36.712][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 20:13:36.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.716][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:36.717][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 20:13:36.720][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 20:13:36.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.723][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 20:13:36.724][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 20:13:36.724][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 20:13:36.725][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 20:13:36.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:36.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:36.729][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 20:13:36.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.732][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 20:13:36.733][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.734][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:36.735][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.735][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.736][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.738][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:36.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:36.740][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.741][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 20:13:36.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:36.743][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.744][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.745][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:36.745][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:36.745][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:36.745][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:36.745][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:36.746][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:36.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:36.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:36.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:36.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:36.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:36.751][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.752][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.753][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:36.754][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:36.755][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.756][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.757][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 20:13:36.759][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.760][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:36.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.761][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:36.762][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.763][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.764][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.766][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:36.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:36.768][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.769][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 20:13:36.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:36.771][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.772][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.773][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:36.773][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:36.773][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:36.773][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:36.773][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:36.774][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:36.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:36.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:36.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:36.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:36.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:36.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.780][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.982][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:36.983][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:36.984][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.985][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:36.986][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 20:13:36.987][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.988][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 20:13:36.989][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:36.991][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:36.992][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.993][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:36.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:36.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:36.997][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:36.997][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 20:13:36.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:36.999][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.000][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.001][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.002][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:37.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.004][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:37.005][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.007][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.008][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.009][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:37.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:37.010][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.011][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.012][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 20:13:37.014][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.015][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:37.016][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:37.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.021][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:37.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:37.023][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.024][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 20:13:37.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:37.026][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.026][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.027][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:37.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:37.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.034][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:37.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:37.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.037][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:37.039][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:37.039][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.040][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 20:13:37.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.043][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 20:13:37.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.047][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 20:13:37.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.048][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 20:13:37.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.052][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 20:13:37.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.065][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 20:13:37.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.075][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 20:13:37.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.077][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 20:13:37.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.083][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 20:13:37.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.100][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 20:13:37.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.110][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 20:13:37.112][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 20:13:37.113][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 20:13:37.115][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 20:13:37.116][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:37.117][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 20:13:37.119][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:37.120][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:37.121][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 20:13:37.123][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 20:13:37.124][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:37.125][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 20:13:37.126][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:37.128][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:37.129][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 20:13:37.130][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 20:13:37.132][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 20:13:37.133][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 20:13:37.134][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:37.136][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 20:13:37.137][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 20:13:37.138][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 20:13:37.140][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 20:13:37.141][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 20:13:37.143][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 20:13:37.144][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 20:13:37.145][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 20:13:37.147][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 20:13:37.148][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 20:13:37.150][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 20:13:37.151][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 20:13:37.153][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 20:13:37.154][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 20:13:37.156][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 20:13:37.157][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 20:13:37.159][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 20:13:37.160][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 20:13:37.162][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 20:13:37.163][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 20:13:37.165][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 20:13:37.166][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 20:13:37.168][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 20:13:37.169][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 20:13:37.171][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 20:13:37.172][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 20:13:37.174][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 20:13:37.175][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 20:13:37.177][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 20:13:37.178][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 20:13:37.180][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 20:13:37.181][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 20:13:37.183][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 20:13:37.184][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 20:13:37.186][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 20:13:37.187][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 20:13:37.189][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 20:13:37.190][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 20:13:37.192][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 20:13:37.193][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 20:13:37.195][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 20:13:37.196][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 20:13:37.197][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 20:13:37.199][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 20:13:37.200][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 20:13:37.202][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 20:13:37.203][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 20:13:37.205][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:37.206][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:37.208][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 20:13:37.209][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 20:13:37.211][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 20:13:37.212][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 20:13:37.214][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 20:13:37.215][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 20:13:37.217][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 20:13:37.218][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 20:13:37.220][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 20:13:37.221][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 20:13:37.223][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 20:13:37.224][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 20:13:37.226][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 20:13:37.227][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 20:13:37.229][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 20:13:37.230][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 20:13:37.232][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:37.233][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:37.234][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.235][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 20:13:37.236][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.237][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 20:13:37.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.261][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 20:13:37.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.268][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 20:13:37.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.275][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 20:13:37.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.291][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 20:13:37.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.321][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 20:13:37.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.331][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 20:13:37.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.337][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 20:13:37.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:37.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:37.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:37.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:37.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:37.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:37.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:37.344][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 20:13:37.345][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:37.347][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 20:13:37.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.349][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.350][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:37.352][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.353][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.354][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.355][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 20:13:37.356][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 20:13:37.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:37.358][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.359][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 20:13:37.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 20:13:37.360][self$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 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 20:13:37.360][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 20:13:37.361][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:37.362][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:37.362][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:37.362][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:37.363][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 20:13:37.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.366][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:37.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:37.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:37.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:37.369][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:37.369][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 20:13:37.370][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:37.371][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:37.372][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:37.373][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 20:13:37.373][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 20:13:37.374][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:37.376][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:37.377][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 20:13:37.378][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:37.380][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:37.381][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:37.384][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 20:13:37.385][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 20:13:37.386][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 20:13:37.387][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 20:13:37.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:37.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:37.391][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 20:13:37.392][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 20:13:37.393][biodb::testThat]
biodb.INFO [2025-03-20 20:13:37.394][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-20 20:13:37.395][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:37.395][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:37.399][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 20:13:37.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:37.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:37.404][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-20 20:13:37.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-20 20:13:38.228][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:38.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-20 20:13:38.243][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-20 20:13:38.292][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:38.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:38.299][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:38.301][private$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 20:13:38.638][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 20:13:38.975][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:38.979][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-20 20:13:38.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-20 20:13:38.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:38.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:38.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:38.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.007][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 20:13:39.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:39.014][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:39.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:39.351][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:39.687][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:39.690][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-20 20:13:39.696][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-20 20:13:39.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.753][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.DEBUG[2025-03-20 20:13:39.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:39.762][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:39.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 20:13:39.765][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:39.766][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 20:13:39.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.779][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:39.782][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:39.784][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 20:13:39.785][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:39.786][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 20:13:39.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.796][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 20:13:39.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.807][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 20:13:39.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:39.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:39.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-20 20:13:39.835][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:39.836][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-20 20:13:39.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.848][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:39.851][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:39.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-20 20:13:39.854][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:39.855][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-20 20:13:39.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:39.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:39.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:39.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:39.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:39.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:39.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:39.867][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:39.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:39.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:39.873][private$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 20:13:40.206][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 20:13:40.590][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:40.594][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-20 20:13:40.601][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-20 20:13:40.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:40.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:40.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:40.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:40.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:40.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:40.621][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.INFO [2025-03-20 20:13:40.632][biodb::testThat]
biodb.INFO [2025-03-20 20:13:40.633][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-20 20:13:40.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:40.637][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:40.641][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 20:13:40.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:40.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:40.650][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:40.991][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:41.326][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:41.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-20 20:13:41.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-20 20:13:41.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:41.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:41.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:41.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:41.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:41.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:41.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:41.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:41.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:41.378][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:41.381][private$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 20:13:41.716][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 20:13:42.057][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:42.060][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-20 20:13:42.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-20 20:13:42.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:42.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.072][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 20:13:42.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 20:13:42.079][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 20:13:42.080][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 20:13:42.081][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 20:13:42.082][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 20:13:42.082][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.084][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.086][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.087][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.INFO [2025-03-20 20:13:42.090][biodb::testContext]
biodb.INFO [2025-03-20 20:13:42.091][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:42.092][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-20 20:13:42.093][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:42.093][biodb::testContext]
biodb.INFO [2025-03-20 20:13:42.105][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:42.111][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:42.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:42.118][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 20:13:42.119][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.123][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 20:13:42.124][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.127][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 20:13:42.128][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 20:13:42.129][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.133][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 20:13:42.134][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 20:13:42.135][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 20:13:42.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.139][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 20:13:42.140][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 20:13:42.141][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.145][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 20:13:42.146][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 20:13:42.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.149][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 20:13:42.150][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 20:13:42.151][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 20:13:42.152][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 20:13:42.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.156][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 20:13:42.157][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.160][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 20:13:42.161][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 20:13:42.162][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 20:13:42.163][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 20:13:42.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.167][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:42.168][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 20:13:42.169][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 20:13:42.170][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 20:13:42.171][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 20:13:42.172][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 20:13:42.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.174][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 20:13:42.175][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 20:13:42.177][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 20:13:42.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.180][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 20:13:42.181][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 20:13:42.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.185][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 20:13:42.186][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 20:13:42.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.190][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 20:13:42.191][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 20:13:42.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.193][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 20:13:42.194][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 20:13:42.195][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 20:13:42.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.199][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:42.200][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 20:13:42.203][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 20:13:42.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.207][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 20:13:42.208][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 20:13:42.210][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 20:13:42.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.214][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 20:13:42.216][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.217][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-20 20:13:42.218][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:42.220][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.222][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.223][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.224][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:42.225][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:42.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.227][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 20:13:42.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:42.229][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.230][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.231][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:42.231][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:42.231][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:42.231][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:42.231][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:42.232][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:42.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.235][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:42.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.239][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.240][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:42.241][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:42.242][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.243][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.244][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 20:13:42.246][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.247][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:42.248][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:42.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.251][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.252][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.254][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:42.256][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:42.257][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.258][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 20:13:42.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:42.260][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.261][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.262][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:42.262][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:42.262][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:42.262][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:42.262][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:42.263][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:42.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:42.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.270][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:42.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:42.273][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.274][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.275][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 20:13:42.320][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.321][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-20 20:13:42.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.323][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:42.324][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.328][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:42.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:42.330][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.331][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 20:13:42.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:42.333][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.334][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.335][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:42.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:42.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.341][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.342][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.343][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:42.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:42.345][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.346][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.348][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 20:13:42.350][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.351][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:42.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:42.353][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.355][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.357][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:42.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:42.359][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.360][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 20:13:42.361][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:42.362][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.364][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.365][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:42.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.368][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:42.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.371][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.372][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.373][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:42.373][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:42.374][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.375][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:42.377][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:42.378][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.378][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 20:13:42.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.387][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 20:13:42.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.411][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 20:13:42.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.423][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 20:13:42.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.434][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 20:13:42.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.438][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 20:13:42.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.440][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 20:13:42.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.460][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 20:13:42.462][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 20:13:42.463][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 20:13:42.464][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 20:13:42.466][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:42.467][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 20:13:42.468][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:42.470][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:42.471][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 20:13:42.472][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 20:13:42.474][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:42.475][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 20:13:42.476][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:42.477][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:42.479][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 20:13:42.480][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 20:13:42.481][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 20:13:42.483][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 20:13:42.484][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:42.485][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 20:13:42.487][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 20:13:42.488][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 20:13:42.489][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 20:13:42.490][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 20:13:42.492][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 20:13:42.493][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 20:13:42.494][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 20:13:42.495][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 20:13:42.497][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 20:13:42.498][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 20:13:42.499][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 20:13:42.500][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 20:13:42.502][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 20:13:42.503][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 20:13:42.504][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 20:13:42.505][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 20:13:42.507][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 20:13:42.508][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 20:13:42.509][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 20:13:42.511][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 20:13:42.512][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 20:13:42.513][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 20:13:42.514][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 20:13:42.516][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 20:13:42.517][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 20:13:42.518][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 20:13:42.519][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 20:13:42.521][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 20:13:42.522][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 20:13:42.523][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 20:13:42.524][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 20:13:42.526][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 20:13:42.527][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 20:13:42.528][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 20:13:42.529][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 20:13:42.531][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 20:13:42.532][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 20:13:42.533][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 20:13:42.535][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 20:13:42.536][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 20:13:42.537][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 20:13:42.538][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 20:13:42.540][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 20:13:42.541][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 20:13:42.542][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 20:13:42.543][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 20:13:42.545][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:42.546][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:42.547][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 20:13:42.548][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 20:13:42.550][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 20:13:42.551][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 20:13:42.552][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 20:13:42.553][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 20:13:42.555][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 20:13:42.556][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 20:13:42.557][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 20:13:42.558][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 20:13:42.560][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 20:13:42.561][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 20:13:42.562][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 20:13:42.563][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 20:13:42.565][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 20:13:42.566][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 20:13:42.567][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:42.568][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:42.569][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.570][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 20:13:42.571][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.577][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 20:13:42.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.583][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 20:13:42.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.592][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 20:13:42.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.594][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 20:13:42.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.616][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 20:13:42.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.631][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 20:13:42.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.633][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 20:13:42.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:42.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:42.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:42.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:42.670][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 20:13:42.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:42.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:42.673][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:42.674][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 20:13:42.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.677][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.678][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.679][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:42.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.680][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.681][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.682][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 20:13:42.683][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 20:13:42.684][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:42.685][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.686][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 20:13:42.687][self$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 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 20:13:42.687][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 20:13:42.688][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:42.689][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:42.689][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:42.689][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:42.690][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 20:13:42.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.693][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:42.694][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:42.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:42.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:42.696][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:42.696][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 20:13:42.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:42.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:42.699][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:42.700][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 20:13:42.700][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 20:13:42.701][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:42.702][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:42.704][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 20:13:42.705][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:42.706][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:42.708][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:42.711][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 20:13:42.712][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 20:13:42.713][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 20:13:42.715][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 20:13:42.716][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:42.717][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:42.718][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 20:13:42.719][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 20:13:42.720][biodb::testThat]
biodb.INFO [2025-03-20 20:13:42.721][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-20 20:13:42.722][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:42.723][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:42.726][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 20:13:42.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:42.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 20:13:42.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:42.733][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 20:13:42.737][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 20:13:42.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:42.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:42.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-20 20:13:43.077][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-20 20:13:43.411][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:43.415][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-20 20:13:43.423][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-20 20:13:43.437][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 20:13:43.439][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 20:13:43.441][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 20:13:43.443][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 20:13:43.444][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.447][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.450][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-20 20:13:43.458][biodb::testContext]
biodb.INFO [2025-03-20 20:13:43.459][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:43.460][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-20 20:13:43.462][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-20 20:13:43.463][biodb::testContext]
biodb.INFO [2025-03-20 20:13:43.466][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:43.468][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:43.473][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:43.474][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-20 20:13:43.475][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.481][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-20 20:13:43.482][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.485][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-20 20:13:43.486][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.490][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-20 20:13:43.491][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-20 20:13:43.492][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-20 20:13:43.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.495][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-20 20:13:43.496][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-20 20:13:43.497][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.500][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-20 20:13:43.501][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-20 20:13:43.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.504][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-20 20:13:43.505][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-20 20:13:43.506][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-20 20:13:43.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.509][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.DEBUG[2025-03-20 20:13:43.509][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-20 20:13:43.510][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.514][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-20 20:13:43.515][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-20 20:13:43.516][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-20 20:13:43.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.519][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:43.520][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-20 20:13:43.521][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-20 20:13:43.522][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-20 20:13:43.522][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-20 20:13:43.523][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-20 20:13:43.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.527][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-20 20:13:43.528][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-20 20:13:43.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.531][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-20 20:13:43.532][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-20 20:13:43.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.535][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-20 20:13:43.536][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-20 20:13:43.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.539][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 20:13:43.539][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-20 20:13:43.540][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-20 20:13:43.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.544][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-20 20:13:43.545][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-20 20:13:43.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.548][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-20 20:13:43.549][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-20 20:13:43.552][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-20 20:13:43.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.556][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-20 20:13:43.556][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-20 20:13:43.557][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-20 20:13:43.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.560][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 20:13:43.561][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-20 20:13:43.563][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.564][self$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 20:13:43.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:43.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.570][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:43.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:43.572][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.573][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-20 20:13:43.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:43.575][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:43.576][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:43.577][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:43.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:43.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.583][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:43.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:43.586][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.587][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.588][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-20 20:13:43.590][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.591][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:43.600][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.601][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:43.602][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.603][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.604][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.605][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.605][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:43.606][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:43.607][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.608][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-20 20:13:43.609][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:43.610][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.611][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.612][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:43.612][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:43.612][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:43.612][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-20 20:13:43.612][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-20 20:13:43.613][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:43.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:43.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.618][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.619][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:43.620][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:43.621][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.622][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.623][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-20 20:13:43.625][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.626][self$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 20:13:43.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:43.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-20 20:13:43.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:43.634][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.635][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-20 20:13:43.635][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:43.636][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.637][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.638][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.639][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:43.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:43.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.645][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.646][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:43.646][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:43.647][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.648][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.649][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-20 20:13:43.651][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.652][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-20 20:13:43.653][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.654][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:43.655][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.656][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.658][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-20 20:13:43.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:43.660][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.661][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-20 20:13:43.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:43.663][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.664][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.665][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.665][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-20 20:13:43.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:43.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.670][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.671][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.672][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:43.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:43.674][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.675][self$setPropertyValue]
biodb.DEBUG[2025-03-20 20:13:43.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:43.677][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.680][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 20:13:43.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.681][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 20:13:43.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.684][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 20:13:43.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.692][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 20:13:43.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.693][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 20:13:43.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.722][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 20:13:43.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.728][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 20:13:43.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.734][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 20:13:43.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.747][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-20 20:13:43.748][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-20 20:13:43.749][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-20 20:13:43.751][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-20 20:13:43.752][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:43.753][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-20 20:13:43.754][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:43.756][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:43.757][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-20 20:13:43.758][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-20 20:13:43.759][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:43.761][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-20 20:13:43.762][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-20 20:13:43.763][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-20 20:13:43.764][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-20 20:13:43.766][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-20 20:13:43.767][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-20 20:13:43.768][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-20 20:13:43.769][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:43.771][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-20 20:13:43.772][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-20 20:13:43.773][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-20 20:13:43.774][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-20 20:13:43.776][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-20 20:13:43.777][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-20 20:13:43.778][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-20 20:13:43.779][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-20 20:13:43.781][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-20 20:13:43.782][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-20 20:13:43.783][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-20 20:13:43.784][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-20 20:13:43.786][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-20 20:13:43.787][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-20 20:13:43.788][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-20 20:13:43.789][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-20 20:13:43.791][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-20 20:13:43.792][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-20 20:13:43.793][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-20 20:13:43.795][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-20 20:13:43.796][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-20 20:13:43.797][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-20 20:13:43.798][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-20 20:13:43.800][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-20 20:13:43.801][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-20 20:13:43.802][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-20 20:13:43.803][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-20 20:13:43.805][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-20 20:13:43.806][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-20 20:13:43.807][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-20 20:13:43.809][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-20 20:13:43.810][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-20 20:13:43.811][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-20 20:13:43.812][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-20 20:13:43.814][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-20 20:13:43.815][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-20 20:13:43.816][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-20 20:13:43.817][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-20 20:13:43.819][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-20 20:13:43.820][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-20 20:13:43.821][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-20 20:13:43.822][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-20 20:13:43.824][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-20 20:13:43.825][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-20 20:13:43.826][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-20 20:13:43.827][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-20 20:13:43.829][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-20 20:13:43.830][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:43.831][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:43.832][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-20 20:13:43.834][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-20 20:13:43.835][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-20 20:13:43.836][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-20 20:13:43.837][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-20 20:13:43.839][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-20 20:13:43.840][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-20 20:13:43.841][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-20 20:13:43.843][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-20 20:13:43.844][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-20 20:13:43.845][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-20 20:13:43.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-20 20:13:43.848][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-20 20:13:43.849][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-20 20:13:43.850][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-20 20:13:43.851][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-20 20:13:43.853][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-20 20:13:43.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-20 20:13:43.855][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.855][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 20:13:43.856][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.863][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 20:13:43.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.888][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 20:13:43.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.895][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 20:13:43.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.899][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 20:13:43.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.904][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 20:13:43.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.906][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 20:13:43.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.910][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 20:13:43.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.915][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 20:13:43.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.928][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 20:13:43.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.939][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.DEBUG[2025-03-20 20:13:43.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:43.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.948][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 20:13:43.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:43.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-20 20:13:43.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:43.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:43.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:43.953][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 20:13:43.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:43.955][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 20:13:43.956][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-20 20:13:43.958][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-20 20:13:43.959][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.960][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-20 20:13:43.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.965][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.966][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-20 20:13:43.967][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-20 20:13:43.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-20 20:13:43.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.969][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-20 20:13:43.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-20 20:13:43.971][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-20 20:13:43.972][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-20 20:13:43.973][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-20 20:13:43.973][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-20 20:13:43.973][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-20 20:13:43.974][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-20 20:13:43.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-20 20:13:43.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-20 20:13:43.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-20 20:13:43.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-20 20:13:43.980][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:43.980][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-20 20:13:43.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-20 20:13:43.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-20 20:13:43.982][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-20 20:13:43.983][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-20 20:13:43.983][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-20 20:13:43.984][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-20 20:13:43.986][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-20 20:13:43.987][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-20 20:13:43.989][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-20 20:13:43.990][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-20 20:13:43.992][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-20 20:13:43.995][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-20 20:13:43.996][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-20 20:13:43.997][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-20 20:13:43.998][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-20 20:13:43.999][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:44.000][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-20 20:13:44.001][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-20 20:13:44.002][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-20 20:13:44.004][biodb::testThat]
biodb.INFO [2025-03-20 20:13:44.004][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-20 20:13:44.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-20 20:13:44.006][biodb::testThat]
biodb.DEBUG[2025-03-20 20:13:44.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-20 20:13:44.012][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:44.014][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-20 20:13:44.015][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:44.016][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-20 20:13:44.019][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-20 20:13:44.022][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-20 20:13:44.023][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-20 20:13:44.024][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-20 20:13:44.026][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-20 20:13:44.030][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-20 20:13:44.030][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-20 20:13:44.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-20 20:13:44.033][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-20 20:13:44.034][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-20 20:13:44.035][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-20 20:13:44.036][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-20 20:13:44.037][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-20 20:13:44.038][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-20 20:13:44.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:44.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:44.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:44.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:44.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:44.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:44.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-20 20:13:44.050][scheduler$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 20:13:44.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-20 20:13:44.053][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-20 20:13:44.054][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-20 20:13:44.392][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-20 20:13:45.432][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-20 20:13:45.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-20 20:13:45.444][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-20 20:13:45.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-20 20:13:45.453][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-20 20:13:45.456][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-20 20:13:45.458][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-20 20:13:45.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-20 20:13:45.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:45.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:45.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:45.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-20 20:13:45.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:45.477][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.TRACE[2025-03-20 20:13:45.483][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.485][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.494][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:45.495][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:45.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.499][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-20 20:13:45.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-20 20:13:45.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.503][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:45.505][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:45.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-20 20:13:45.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-20 20:13:45.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.512][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-20 20:13:45.513][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-20 20:13:45.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.517][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-20 20:13:45.518][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-20 20:13:45.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.521][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:45.522][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:45.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.526][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:45.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-20 20:13:45.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.530][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:45.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:45.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.534][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-20 20:13:45.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-20 20:13:45.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:45.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:45.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:45.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-20 20:13:45.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.546][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:45.547][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:45.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-20 20:13:45.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-20 20:13:45.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.555][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:45.556][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:45.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.560][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-20 20:13:45.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-20 20:13:45.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.575][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:45.576][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:45.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-20 20:13:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-20 20:13:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-20 20:13:45.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-20 20:13:45.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-20 20:13:45.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-20 20:13:45.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-20 20:13:45.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-20 20:13:45.621][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-20 20:13:45.625][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-20 20:13:45.626][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-20 20:13:45.627][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-20 20:13:45.628][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-20 20:13:45.629][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-20 20:13:45.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-20 20:13:45.637][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-20 20:13:45.639][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 20:13:45.640][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-20 20:13:45.641][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
22.653 0.951 52.511
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.862 | 0.095 | 1.776 | |
| ChebiEntry | 0.149 | 0.004 | 0.152 | |