Pierrick Roger
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:39 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 201/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2025-01-10 20:14:52 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 20:16:48 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 116.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.21-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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 [2025-01-10 20:15:33.517][biodb::testContext]
biodb.INFO [2025-01-10 20:15:33.519][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:15:33.520][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-01-10 20:15:33.521][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:15:33.522][biodb::testContext]
biodb.INFO [2025-01-10 20:15:33.527][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:15:33.529][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-10 20:15:33.535][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:15:33.536][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-10 20:15:33.537][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.541][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-10 20:15:33.558][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.562][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-10 20:15:33.563][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.566][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-10 20:15:33.567][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-10 20:15:33.568][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-10 20:15:33.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.571][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-10 20:15:33.572][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-10 20:15:33.573][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.577][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-10 20:15:33.578][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-10 20:15:33.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.580][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[2025-01-10 20:15:33.581][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-10 20:15:33.582][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-10 20:15:33.583][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-10 20:15:33.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.586][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-10 20:15:33.587][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.591][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-10 20:15:33.592][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-10 20:15:33.593][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-10 20:15:33.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.596][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:15:33.597][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-10 20:15:33.598][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-10 20:15:33.599][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-10 20:15:33.600][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-10 20:15:33.601][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-10 20:15:33.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.604][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-10 20:15:33.605][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-10 20:15:33.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.609][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-10 20:15:33.610][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-10 20:15:33.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.613][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-10 20:15:33.614][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-10 20:15:33.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.618][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-10 20:15:33.619][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-10 20:15:33.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.622][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-10 20:15:33.623][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-10 20:15:33.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.627][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:15:33.628][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-10 20:15:33.633][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-10 20:15:33.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.636][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-10 20:15:33.637][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-10 20:15:33.638][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-10 20:15:33.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.644][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-10 20:15:33.675][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.697][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-10 20:15:33.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.699][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:15:33.700][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.704][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:15:33.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:15:33.705][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.706][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-10 20:15:33.707][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:15:33.708][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.709][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.710][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:15:33.710][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:15:33.710][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:15:33.710][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:15:33.710][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:15:33.711][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:15:33.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:15:33.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.716][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.717][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.718][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:15:33.719][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:15:33.720][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.721][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.722][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-10 20:15:33.723][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.724][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:15:33.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:15:33.727][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.728][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.729][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.730][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.731][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:15:33.732][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:15:33.733][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.734][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-10 20:15:33.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:15:33.736][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.736][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.737][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:15:33.737][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:15:33.737][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:15:33.737][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:15:33.737][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:15:33.738][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:15:33.739][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.740][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.741][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:15:33.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.744][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.745][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:15:33.746][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:15:33.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.749][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.751][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-10 20:15:33.755][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.757][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-10 20:15:33.758][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:15:33.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.764][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:15:33.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:15:33.771][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.772][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-10 20:15:33.773][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:15:33.774][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.776][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.777][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.778][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:15:33.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.781][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:15:33.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.785][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:15:33.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:15:33.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.789][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.791][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-10 20:15:33.793][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.794][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:15:33.795][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.796][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:15:33.797][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.798][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.799][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.800][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.801][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:15:33.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:15:33.803][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.804][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-10 20:15:33.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:15:33.806][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.807][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:33.808][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.810][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:15:33.811][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:15:33.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:33.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:33.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:15:33.816][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.817][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:15:33.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:15:33.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:33.820][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:15:33.825][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:15:33.826][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.846][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[2025-01-10 20:15:33.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.860][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[2025-01-10 20:15:33.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.878][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[2025-01-10 20:15:33.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:33.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:33.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:33.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:33.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:33.921][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-10 20:15:33.926][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-10 20:15:33.927][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-10 20:15:33.929][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-10 20:15:33.930][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:15:33.932][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-10 20:15:33.933][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-10 20:15:33.935][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-10 20:15:33.937][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-10 20:15:33.938][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-10 20:15:33.940][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:15:33.941][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-10 20:15:33.943][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-10 20:15:33.944][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-10 20:15:33.946][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-10 20:15:33.947][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-10 20:15:33.948][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-10 20:15:33.950][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-10 20:15:33.951][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:15:33.953][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-10 20:15:33.954][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-10 20:15:33.956][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-10 20:15:33.957][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-10 20:15:33.959][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-10 20:15:33.960][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-10 20:15:33.962][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-10 20:15:33.963][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-10 20:15:33.964][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-10 20:15:33.966][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-10 20:15:33.967][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-10 20:15:33.969][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-10 20:15:33.970][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-10 20:15:33.971][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-10 20:15:33.973][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-10 20:15:33.974][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-10 20:15:33.975][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-10 20:15:33.977][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-10 20:15:33.978][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-10 20:15:33.979][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-10 20:15:33.981][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-10 20:15:33.982][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-10 20:15:33.983][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-10 20:15:33.985][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-10 20:15:33.986][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-10 20:15:33.987][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-10 20:15:33.989][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-10 20:15:33.990][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-10 20:15:33.991][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-10 20:15:33.993][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-10 20:15:33.994][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-10 20:15:33.995][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-10 20:15:33.997][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-10 20:15:33.998][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-10 20:15:33.999][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-10 20:15:34.000][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-10 20:15:34.002][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-10 20:15:34.003][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-10 20:15:34.004][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-10 20:15:34.006][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-10 20:15:34.007][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-10 20:15:34.008][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-10 20:15:34.010][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-10 20:15:34.011][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-10 20:15:34.012][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-10 20:15:34.013][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-10 20:15:34.015][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-10 20:15:34.016][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:15:34.017][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:15:34.019][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-10 20:15:34.020][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-10 20:15:34.021][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-10 20:15:34.023][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-10 20:15:34.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-10 20:15:34.025][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-10 20:15:34.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-10 20:15:34.028][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-10 20:15:34.029][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-10 20:15:34.030][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-10 20:15:34.032][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-10 20:15:34.033][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-10 20:15:34.034][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-10 20:15:34.036][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-10 20:15:34.037][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-10 20:15:34.043][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-10 20:15:34.044][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:15:34.047][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:15:34.048][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.050][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.051][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[2025-01-10 20:15:34.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.113][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[2025-01-10 20:15:34.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.126][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.DEBUG[2025-01-10 20:15:34.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.132][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[2025-01-10 20:15:34.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.138][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[2025-01-10 20:15:34.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.144][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[2025-01-10 20:15:34.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:15:34.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:34.163][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-10 20:15:34.173][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-10 20:15:34.175][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:34.176][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-10 20:15:34.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:34.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:15:34.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:34.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:15:34.181][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:34.182][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-10 20:15:34.182][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-10 20:15:34.183][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:15:34.184][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:34.185][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-10 20:15:34.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-10 20:15:34.187][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-10 20:15:34.188][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-10 20:15:34.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:15:34.189][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:15:34.189][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:15:34.190][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-10 20:15:34.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:34.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:34.193][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:15:34.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:15:34.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:15:34.196][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:15:34.197][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:34.197][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-10 20:15:34.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:15:34.198][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:15:34.199][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-10 20:15:34.200][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-10 20:15:34.200][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-10 20:15:34.206][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:15:34.208][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:15:34.210][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-10 20:15:34.211][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:15:34.212][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:15:34.214][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:15:34.235][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-10 20:15:34.236][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-10 20:15:34.240][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-10 20:15:34.244][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-10 20:15:34.254][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:15:34.255][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:15:34.256][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-10 20:15:34.257][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-10 20:15:34.265][biodb::testThat]
biodb.INFO [2025-01-10 20:15:34.266][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-01-10 20:15:34.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:34.268][biodb::testThat]
biodb.TRACE[2025-01-10 20:15:34.272][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-01-10 20:15:34.274][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:34.277][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:34.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:34.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:34.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:34.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:34.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:34.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:34.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:34.309][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.312][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.329][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.330][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.332][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.363][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.366][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.371][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:34.372][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:34.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.374][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:34.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:34.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.379][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.380][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.382][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.383][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.387][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.388][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.390][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.395][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:34.397][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.398][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:34.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.406][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.453][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.454][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.456][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.461][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:34.462][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.464][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.465][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:34.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.469][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.470][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.472][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:34.546][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-01-10 20:15:34.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:34.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:34.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:34.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:34.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:34.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:34.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.602][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:34.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:34.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.606][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:34.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:34.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:34.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.705][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.708][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:34.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:34.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.737][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.738][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.739][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:34.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.763][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.766][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:34.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.789][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.792][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:34.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:34.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.815][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.816][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.818][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.841][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.844][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:34.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.860][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.864][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.872][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.872][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.874][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:34.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:34.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.890][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.898][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.899][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.901][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:34.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.913][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.924][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.925][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.927][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.928][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:34.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.943][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.951][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.952][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.954][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:34.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:34.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.977][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.978][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.980][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:34.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:34.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.007][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.008][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.010][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.022][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.025][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.029][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:35.030][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:35.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.032][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.036][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:35.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:35.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.039][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.043][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.044][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.046][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.050][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.053][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.058][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.060][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.064][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.065][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.067][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.071][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.072][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.074][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.078][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-01-10 20:15:35.079][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:35.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.081][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.085][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.088][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.092][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:35.093][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:35.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.095][ef$get] fields variable is a list.
biodb.INFO [2025-01-10 20:15:35.101][biodb::testThat]
biodb.INFO [2025-01-10 20:15:35.102][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-10 20:15:35.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:35.104][biodb::testThat]
biodb.DEBUG[2025-01-10 20:15:35.117][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-01-10 20:15:35.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:35.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-01-10 20:15:35.129][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:15:35.130][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-01-10 20:15:35.137][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:35.160][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:35.161][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:35.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:35.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:35.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:35.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:35.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:35.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:35.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:35.174][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.177][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.198][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:35.200][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:35.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.202][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.203][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:35.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:35.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.207][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:35.208][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:35.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.209][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:35.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:35.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.215][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.217][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:35.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:35.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.223][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.225][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.230][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.231][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.233][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.234][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:35.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.238][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:35.239][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.241][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.242][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:35.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.246][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.249][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.254][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.255][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.262][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:35.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:35.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.270][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:35.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:35.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.275][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:35.276][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:35.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.278][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:35.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:35.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:35.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:35.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:35.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:35.322][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-01-10 20:15:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-10 20:15:35.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-10 20:15:35.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-10 20:15:35.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-10 20:15:35.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-10 20:15:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-10 20:15:35.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:15:35.342][biodb::testThat]
biodb.INFO [2025-01-10 20:15:35.342][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-10 20:15:35.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:35.344][biodb::testThat]
biodb.TRACE[2025-01-10 20:15:35.347][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.348][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.350][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:35.351][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-01-10 20:15:35.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:35.391][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-01-10 20:15:35.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-10 20:15:35.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:15:35.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-10 20:15:35.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:15:35.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-10 20:15:35.461][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[2025-01-10 20:15:35.465][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:15:35.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:15:35.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:15:35.469][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-10 20:15:35.472][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-01-10 20:15:35.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.484][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:35.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.486][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.487][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:35.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.490][ef$get] fields variable is a list.
biodb.INFO [2025-01-10 20:15:35.493][biodb::testThat]
biodb.INFO [2025-01-10 20:15:35.494][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-01-10 20:15:35.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:35.496][biodb::testThat]
biodb.TRACE[2025-01-10 20:15:35.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.531][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:35.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:35.592][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.INFO [2025-01-10 20:15:35.595][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-01-10 20:15:35.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:35.597][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:35.599][private$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[2025-01-10 20:15:36.264][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[2025-01-10 20:15:36.719][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:36.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-10 20:15:36.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.INFO [2025-01-10 20:15:36.751][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.752][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-01-10 20:15:36.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:36.754][biodb::testThat]
biodb.TRACE[2025-01-10 20:15:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:36.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:36.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:36.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:36.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.807][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.814][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:36.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:36.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:36.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:36.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:36.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:36.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:36.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:36.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:36.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.866][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-10 20:15:36.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:36.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-10 20:15:36.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:36.877][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:36.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-10 20:15:36.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:36.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:15:36.886][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.886][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-10 20:15:36.887][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:36.888][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.896][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.897][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-10 20:15:36.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:36.899][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.906][biodb::testThat]
biodb.INFO [2025-01-10 20:15:36.907][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-10 20:15:36.908][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:36.909][biodb::testThat]
biodb.DEBUG[2025-01-10 20:15:36.912][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-01-10 20:15:37.917][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-01-10 20:15:39.546][biodb::testThat]
biodb.INFO [2025-01-10 20:15:39.548][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-10 20:15:39.549][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:39.550][biodb::testThat]
biodb.DEBUG[2025-01-10 20:15:39.990][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[2025-01-10 20:15:40.456][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:40.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:40.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:40.461][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:40.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:40.464][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:40.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:40.467][ef$get] fields variable is a list.
biodb.INFO [2025-01-10 20:15:40.470][biodb::testThat]
biodb.INFO [2025-01-10 20:15:40.471][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-01-10 20:15:40.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:15:40.474][biodb::testThat]
biodb.TRACE[2025-01-10 20:15:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:40.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:40.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:40.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:40.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:40.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:40.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:40.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:40.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:40.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:40.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:40.596][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.INFO [2025-01-10 20:15:40.599][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-01-10 20:15:40.620][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:40.621][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:40.636][private$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[2025-01-10 20:15:41.188][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[2025-01-10 20:15:41.974][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:41.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-01-10 20:15:41.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-01-10 20:15:42.087][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[2025-01-10 20:15:42.090][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:15:42.091][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:15:42.093][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:15:42.094][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-01-10 20:15:42.107][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-10 20:15:42.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-10 20:15:42.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:42.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:42.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:42.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:42.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:42.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:42.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:42.140][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[2025-01-10 20:15:42.143][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:42.144][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:42.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:15:42.500][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:15:43.104][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:43.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-01-10 20:15:43.116][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-01-10 20:15:43.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:43.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:43.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:43.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:43.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:43.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:43.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:43.157][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-01-10 20:15:43.210][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:43.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-01-10 20:15:43.213][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:43.214][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:43.216][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:43.217][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:43.218][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:43.218][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:43.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:43.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:43.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:43.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:43.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:43.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:43.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:43.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-01-10 20:15:43.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:43.234][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:43.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-01-10 20:15:43.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-01-10 20:15:43.936][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:43.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-01-10 20:15:43.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-01-10 20:15:43.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-01-10 20:15:43.956][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:43.957][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:43.958][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:43.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:43.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:43.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:43.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:43.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:43.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:43.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:43.972][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:43.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:43.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:43.975][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:43.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:43.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:43.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:43.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:43.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:43.981][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:43.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:43.983][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:43.985][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:43.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:43.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:43.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:43.990][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:43.991][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:43.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:43.994][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:43.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:43.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.002][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:44.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:44.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.005][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:44.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:44.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:44.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.013][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:44.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.019][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:44.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:44.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.022][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.023][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:44.024][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:44.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:44.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:44.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.034][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.040][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:44.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:44.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.043][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:44.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:44.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.053][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:44.055][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:44.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.057][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.058][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:44.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:44.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.062][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:44.063][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:44.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.065][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:44.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:44.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:44.110][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-01-10 20:15:44.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:44.132][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:15:44.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:44.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:44.138][private$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[2025-01-10 20:15:44.494][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[2025-01-10 20:15:44.848][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:44.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-01-10 20:15:44.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-01-10 20:15:44.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:44.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:44.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:44.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:44.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:44.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:44.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:44.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:44.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:44.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:44.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:44.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:44.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:44.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:44.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:44.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:44.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:44.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:44.902][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-01-10 20:15:44.903][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:44.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-01-10 20:15:44.906][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:44.907][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:44.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:44.909][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:44.910][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:44.911][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:44.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:44.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:44.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:44.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:44.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:44.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:44.937][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[2025-01-10 20:15:44.938][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-01-10 20:15:44.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:44.942][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:44.943][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-01-10 20:15:45.292][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-01-10 20:15:45.653][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:45.655][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-01-10 20:15:45.658][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-01-10 20:15:45.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-01-10 20:15:45.662][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:45.663][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:45.664][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:45.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:45.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:45.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:45.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:45.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:45.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:45.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:45.677][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.678][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.680][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.685][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:45.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:45.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.689][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:45.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:45.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.693][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:45.694][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:45.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.696][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:45.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:45.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.702][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:45.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:45.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.705][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:45.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:45.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:45.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:45.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:45.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:45.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:45.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:45.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.720][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.721][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:45.722][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.724][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.725][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:45.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:45.730][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:45.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.736][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:45.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:45.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.744][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:45.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:45.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.747][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:45.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:45.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:45.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.754][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.756][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:45.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:45.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.759][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:45.760][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:45.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.762][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.763][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:45.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:45.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:45.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:45.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:45.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:45.804][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-01-10 20:15:45.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:45.855][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[2025-01-10 20:15:45.857][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:15:45.859][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:15:45.860][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:15:45.861][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-10 20:15:45.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:45.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:45.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:45.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:45.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:45.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:45.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:45.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:45.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:45.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:45.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:45.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:45.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:45.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:45.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:45.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:45.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:45.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:45.904][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-01-10 20:15:45.905][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:45.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-01-10 20:15:45.909][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:45.910][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:45.911][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:45.913][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:45.914][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:45.915][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:45.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:45.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:45.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:45.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:45.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:45.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:45.928][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[2025-01-10 20:15:45.930][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-01-10 20:15:45.933][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:45.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:45.935][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-01-10 20:15:46.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-01-10 20:15:46.636][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:46.641][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-01-10 20:15:46.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-01-10 20:15:46.655][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-01-10 20:15:46.658][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:46.661][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:46.664][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:46.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:46.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:46.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:46.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:46.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:46.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:46.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:46.715][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.718][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.724][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:46.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:46.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.729][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:46.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:46.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.732][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:46.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:46.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.737][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.739][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:46.740][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:46.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.743][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:46.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:46.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.750][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.752][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:46.754][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.757][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:46.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:46.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.763][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.765][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:46.767][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:46.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.770][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:46.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:46.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:46.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:46.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.783][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.785][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:46.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:46.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.790][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:46.791][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:46.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.794][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:46.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:46.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:46.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:46.852][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-01-10 20:15:46.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:46.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:46.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:46.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:46.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:46.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:46.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:46.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:46.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:46.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:46.891][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.DEBUG[2025-01-10 20:15:46.892][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-01-10 20:15:46.894][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:46.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-01-10 20:15:46.897][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:46.898][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:46.900][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:46.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:46.902][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:46.903][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:46.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:46.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:46.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:46.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:46.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:46.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:46.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:46.920][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-01-10 20:15:46.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:46.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:46.929][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-01-10 20:15:47.295][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-01-10 20:15:47.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:47.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-01-10 20:15:47.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-01-10 20:15:47.689][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-01-10 20:15:47.691][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:47.693][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:47.694][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:47.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:47.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:47.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:47.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:47.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:47.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:47.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:47.721][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.725][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.732][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:47.733][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:47.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.735][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.737][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:47.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:47.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.741][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.742][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:47.744][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:47.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.746][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:47.749][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:47.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.751][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.753][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:47.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:47.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.756][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.758][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:47.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.762][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:47.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:47.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.769][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:47.770][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:47.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.772][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:47.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:47.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.778][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:47.779][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:47.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.781][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.782][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:47.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:47.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:47.787][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:47.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.789][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:47.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:47.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:47.833][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-01-10 20:15:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:47.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:47.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:47.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:47.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:47.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:47.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:47.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:47.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:47.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:47.863][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-01-10 20:15:47.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:47.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-01-10 20:15:47.867][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:47.868][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:47.869][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:47.870][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:47.871][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:47.872][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:47.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:47.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:47.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:47.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:47.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:47.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:47.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:47.884][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-01-10 20:15:47.887][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:47.888][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:47.889][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-01-10 20:15:48.238][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-01-10 20:15:48.593][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:48.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-01-10 20:15:48.606][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-01-10 20:15:48.612][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-01-10 20:15:48.616][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:48.619][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:48.622][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:48.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:48.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:48.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:48.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:48.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:48.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:48.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:48.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.663][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.665][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.672][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:48.673][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:48.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.675][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.677][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:48.678][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:48.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.680][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.682][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:48.683][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:48.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.685][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:48.688][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:48.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.690][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:48.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:48.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.694][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.695][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:48.696][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.698][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:48.701][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:48.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.703][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.704][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:48.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:48.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.707][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:48.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:48.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.713][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:48.714][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:48.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:48.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:48.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:48.723][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:48.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.725][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:48.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:48.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:48.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:48.785][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-01-10 20:15:48.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:48.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:48.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:48.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:48.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:48.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:48.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:48.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:48.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:48.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:48.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:48.851][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-01-10 20:15:48.853][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:48.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-01-10 20:15:48.859][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:48.860][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:48.862][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:48.863][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:48.865][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:48.866][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:48.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:48.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:48.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:48.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:48.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:48.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:48.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:48.888][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-01-10 20:15:48.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:48.895][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:48.897][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-01-10 20:15:49.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-01-10 20:15:49.615][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:49.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-01-10 20:15:49.634][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-01-10 20:15:49.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-01-10 20:15:49.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:49.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:49.655][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:49.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:49.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:49.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:49.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:49.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:49.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:49.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:49.726][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.731][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.739][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:49.740][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:49.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.742][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:49.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:49.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.748][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:49.749][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:49.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.750][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:49.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:49.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.756][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:49.757][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:49.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.759][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:49.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:49.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.764][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:49.765][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:49.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:49.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.772][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:49.773][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:49.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.775][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.780][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:49.781][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.783][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.784][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:49.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.788][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:49.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:49.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.791][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:49.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:49.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.796][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:49.797][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:49.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.798][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:49.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.804][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:49.805][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:49.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.807][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.808][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:49.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:49.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.812][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:49.813][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:49.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.815][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.816][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:49.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:49.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:49.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:49.862][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-01-10 20:15:49.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:49.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:49.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:49.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:49.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:49.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:49.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:49.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:49.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:49.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:49.884][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-01-10 20:15:49.885][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:49.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-01-10 20:15:49.888][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:49.889][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:49.890][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:49.891][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:49.892][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:49.893][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:49.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:49.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:49.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:49.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:49.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:49.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:49.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:49.905][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-01-10 20:15:49.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:49.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:49.914][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-01-10 20:15:50.266][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-01-10 20:15:50.618][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:50.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-01-10 20:15:50.631][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-01-10 20:15:50.637][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-01-10 20:15:50.640][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:50.643][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:50.646][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:50.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:50.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:50.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:50.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:50.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:50.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:50.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:50.673][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.675][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.678][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.686][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:50.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:50.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.690][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.691][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:50.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.697][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:50.698][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:50.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.700][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:50.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:50.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:50.708][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:50.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.710][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.717][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:50.718][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:50.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.720][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:50.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:50.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.726][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:50.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:50.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.730][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.731][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:50.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:50.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.736][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:50.737][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:50.747][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:50.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.750][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.768][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:50.769][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:50.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.771][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:50.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:50.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.777][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:50.778][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:50.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.780][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:50.787][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.789][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:50.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:50.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:50.837][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-01-10 20:15:50.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:50.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:50.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:50.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:50.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:50.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:50.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:50.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:50.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:50.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:50.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:50.862][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-01-10 20:15:50.864][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:50.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-01-10 20:15:50.875][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:50.876][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:50.877][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:50.878][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:50.880][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:50.881][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:50.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:50.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:50.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:50.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:50.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:50.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:50.895][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[2025-01-10 20:15:50.896][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-01-10 20:15:50.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:50.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:50.902][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-01-10 20:15:51.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-01-10 20:15:51.607][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:51.609][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-01-10 20:15:51.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-01-10 20:15:51.617][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-01-10 20:15:51.619][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:51.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:51.621][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:51.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:51.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:51.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:51.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:51.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:51.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:51.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:51.636][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.639][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.645][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:51.646][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:51.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.647][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.649][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:51.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:51.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.653][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:51.654][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:51.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.656][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:51.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:51.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.661][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:51.662][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:51.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.664][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:51.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:51.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.669][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:51.671][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:51.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.672][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:51.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:51.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.688][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:51.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:51.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.692][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.693][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:51.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.696][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.697][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:51.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.701][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:51.702][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:51.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.704][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:51.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:51.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:51.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:51.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.713][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:51.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.718][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:51.719][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:51.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.721][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.722][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:51.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:51.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:51.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:51.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.729][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:51.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:51.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:51.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:51.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:51.773][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-01-10 20:15:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:51.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:51.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:51.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:51.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:51.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:51.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:51.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:51.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:51.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:51.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:51.801][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-01-10 20:15:51.802][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:51.803][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-01-10 20:15:51.804][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:51.805][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:51.807][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:51.808][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:51.809][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:51.809][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:51.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:51.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:51.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:51.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:51.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:51.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:51.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:51.823][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-01-10 20:15:51.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:51.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:51.828][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-01-10 20:15:52.185][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-01-10 20:15:52.554][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:52.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-01-10 20:15:52.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-01-10 20:15:52.568][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-01-10 20:15:52.570][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:52.573][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:52.575][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:52.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:52.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:52.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:52.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:52.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:52.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:52.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:52.597][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.599][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.602][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.610][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:52.612][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:52.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.615][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.617][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:52.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:52.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.624][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:52.626][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:52.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.647][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:52.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:52.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.657][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:52.659][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:52.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.662][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:52.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.671][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:52.673][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:52.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.675][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.681][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:52.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:52.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.684][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.685][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:52.686][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.694][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:52.696][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:52.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.698][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.704][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:52.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:52.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.707][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:52.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:52.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.713][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:52.714][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:52.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.722][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:52.724][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:52.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.726][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.727][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:52.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:52.787][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-01-10 20:15:52.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:52.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:52.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:52.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:52.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:52.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:52.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:52.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:52.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:52.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:52.813][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-01-10 20:15:52.814][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:52.816][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-01-10 20:15:52.817][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:52.819][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:52.820][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:52.821][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:52.822][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:52.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:52.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:52.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:52.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:52.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:52.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:52.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:52.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:52.839][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-01-10 20:15:52.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:52.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:52.844][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-01-10 20:15:53.196][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-01-10 20:15:53.550][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:53.553][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-01-10 20:15:53.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-01-10 20:15:53.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-01-10 20:15:53.565][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:53.567][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:53.568][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:53.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:53.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:53.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:53.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:53.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:53.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:53.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:53.605][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.610][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.618][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:53.619][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:53.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.622][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:53.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:53.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.630][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:53.632][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:53.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.635][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:53.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:53.645][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:53.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.647][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:53.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.655][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:53.657][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:53.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.660][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:53.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.666][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:53.667][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:53.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.669][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.670][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:53.671][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.673][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.674][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:53.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.678][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:53.679][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:53.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.681][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.686][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:53.687][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:53.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.689][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.694][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:53.695][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:53.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.697][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:53.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:53.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.702][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:53.703][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:53.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.706][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.707][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:53.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:53.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:53.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:53.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:53.760][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-01-10 20:15:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:53.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:53.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:53.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:53.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:53.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:53.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:53.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:53.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:53.785][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-01-10 20:15:53.786][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:53.788][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-01-10 20:15:53.789][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:53.791][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:53.792][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:53.801][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:53.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:53.808][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:53.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:53.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:53.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:53.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:53.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:53.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:53.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:53.841][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-01-10 20:15:53.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:53.849][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:53.852][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-01-10 20:15:54.198][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-01-10 20:15:54.618][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:54.630][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-01-10 20:15:54.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-01-10 20:15:54.652][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-01-10 20:15:54.657][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:54.660][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:54.663][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:54.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:54.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:54.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:54.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:54.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:54.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:54.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:54.693][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.694][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.697][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.704][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:54.706][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:54.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.708][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:54.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.715][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:54.717][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:54.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.719][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:54.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:54.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.727][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:54.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:54.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.731][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:54.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:54.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.739][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:54.740][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:54.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.743][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:54.751][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:54.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.753][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.755][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:54.756][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.757][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.759][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:54.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:54.764][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:54.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.766][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:54.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:54.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.771][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:54.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:54.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.774][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.787][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:54.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:54.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.792][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:54.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:54.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.800][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:54.801][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:54.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.804][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:54.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:54.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:54.869][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-01-10 20:15:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:54.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:54.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:54.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:54.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:54.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:54.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:54.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:54.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:54.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:54.893][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-01-10 20:15:54.894][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:54.895][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-01-10 20:15:54.897][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:54.898][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:54.899][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:54.904][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:54.906][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:54.907][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:54.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:54.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:54.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:54.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:54.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:54.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:54.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:54.920][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-01-10 20:15:54.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:54.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:54.925][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-01-10 20:15:55.266][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-01-10 20:15:55.615][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:55.617][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-01-10 20:15:55.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-01-10 20:15:55.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-01-10 20:15:55.624][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:55.625][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:55.627][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:55.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:55.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:55.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:55.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:55.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:55.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:55.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:55.640][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.642][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.648][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:55.649][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:55.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.651][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.652][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:55.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.656][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:55.657][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:55.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.659][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.660][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:55.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:55.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.664][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:55.665][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:55.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.667][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.672][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:55.673][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:55.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.675][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:55.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:55.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:55.681][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:55.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.695][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.696][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:55.698][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.700][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.701][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.705][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:55.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:55.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.708][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:55.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:55.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.713][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:55.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:55.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.716][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:55.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.721][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:55.722][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:55.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.724][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:55.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:55.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:55.730][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:55.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.732][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:55.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:55.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:55.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:55.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:55.776][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-01-10 20:15:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:55.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:55.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:55.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:55.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:55.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:55.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:55.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:55.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:55.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:55.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:55.804][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-01-10 20:15:55.805][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:55.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-01-10 20:15:55.808][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:55.809][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:55.810][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:55.811][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:55.812][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:55.813][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:55.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:55.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:55.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:55.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:55.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:55.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:55.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:55.826][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-01-10 20:15:55.829][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:55.830][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:55.831][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-01-10 20:15:56.201][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-01-10 20:15:56.546][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:56.551][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-01-10 20:15:56.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-01-10 20:15:56.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-01-10 20:15:56.567][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:56.569][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:56.572][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:56.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:56.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:56.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:56.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:56.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:56.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:56.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:56.598][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.600][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.603][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.611][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:56.612][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:56.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.615][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.617][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:56.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:56.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.622][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:56.623][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:56.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.625][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:56.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:56.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:56.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:56.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.644][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:56.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:56.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.648][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.650][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:56.651][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:56.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.654][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:56.655][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.657][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:56.663][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:56.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.665][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:56.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:56.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.670][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:56.671][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:56.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.673][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:56.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:56.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.678][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:56.679][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:56.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.681][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.686][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:56.687][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:56.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.689][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:56.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:56.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:56.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:56.728][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-01-10 20:15:56.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:56.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:56.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:56.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:56.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:56.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:56.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:56.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:56.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:56.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:56.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:56.756][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-01-10 20:15:56.757][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:56.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-01-10 20:15:56.760][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:56.761][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:56.762][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:56.763][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:56.764][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:56.765][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:56.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:56.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:56.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:56.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:56.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:56.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:56.777][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[2025-01-10 20:15:56.778][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-01-10 20:15:56.781][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:56.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:56.783][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-01-10 20:15:57.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-01-10 20:15:57.490][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:57.493][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-01-10 20:15:57.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-01-10 20:15:57.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-01-10 20:15:57.505][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:57.507][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:57.509][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:57.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:57.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:57.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:57.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:57.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:57.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:57.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:57.526][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.527][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.529][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.534][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:57.535][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:57.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:57.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:57.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.556][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:57.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.561][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:57.562][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:57.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.564][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.565][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:57.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:57.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.568][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.569][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:57.570][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:57.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.572][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.573][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:57.575][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.576][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.578][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:57.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:57.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:57.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.585][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:57.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:57.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.590][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:57.591][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:57.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.593][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.598][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:57.599][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:57.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.601][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:57.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.606][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:57.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:57.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.609][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:57.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:57.655][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-01-10 20:15:57.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:57.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:57.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:57.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:57.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:57.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:57.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:57.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:57.677][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[2025-01-10 20:15:57.678][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-01-10 20:15:57.679][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:57.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-01-10 20:15:57.682][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:57.683][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:57.684][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:57.685][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:57.686][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:57.687][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:57.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:57.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:57.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:57.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:57.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:57.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:57.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:57.700][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-01-10 20:15:57.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:57.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:57.705][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-01-10 20:15:58.051][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-01-10 20:15:58.425][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:58.429][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-01-10 20:15:58.437][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-01-10 20:15:58.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-01-10 20:15:58.446][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:58.449][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:58.451][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:58.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:58.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:58.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:58.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:58.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:58.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:58.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:58.478][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.480][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.483][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.501][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:58.503][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:58.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.505][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:58.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.511][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:58.512][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:58.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.514][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.519][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:58.520][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:58.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.522][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:58.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:58.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.527][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:58.528][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:58.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.530][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:58.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:58.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.535][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:58.536][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:58.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.538][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.539][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:58.540][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.542][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:58.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.547][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:58.548][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:58.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.550][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:58.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.555][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:58.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:58.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.558][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:58.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:58.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.563][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:58.564][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:58.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.566][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:58.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.571][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:58.572][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:58.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.574][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:58.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:58.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:58.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:58.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:58.622][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-01-10 20:15:58.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:58.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:58.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:58.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:58.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:58.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:58.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:58.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:58.644][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-01-10 20:15:58.645][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:58.647][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-01-10 20:15:58.648][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:58.649][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:58.650][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:58.651][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:58.652][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:58.653][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:58.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:58.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:58.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:58.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:58.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:58.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:58.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:58.666][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-01-10 20:15:58.668][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:58.669][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:58.670][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-01-10 20:15:59.026][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-01-10 20:15:59.381][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:15:59.386][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-01-10 20:15:59.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-01-10 20:15:59.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-01-10 20:15:59.402][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:15:59.420][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:15:59.423][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:15:59.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:59.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:59.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:59.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:59.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:59.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:59.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:15:59.445][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.449][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.455][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:59.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:59.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.459][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:15:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:15:59.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.465][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:59.466][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:59.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.468][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:15:59.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:15:59.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.474][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:59.475][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:59.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.477][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:15:59.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:15:59.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.482][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:59.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:59.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.485][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:15:59.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:15:59.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:59.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:15:59.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.494][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.495][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:59.496][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.498][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.500][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:15:59.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:59.505][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:59.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.507][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:59.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:15:59.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.512][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:59.513][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:59.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.515][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:15:59.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:15:59.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.520][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:59.521][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:59.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.523][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:15:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:15:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.534][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:59.535][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:59.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.538][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:15:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:15:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:15:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:15:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:15:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:59.584][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-01-10 20:15:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:15:59.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:15:59.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:15:59.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:15:59.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:59.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:59.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:59.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:59.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:59.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:59.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:59.607][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-01-10 20:15:59.608][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:15:59.610][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-01-10 20:15:59.611][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:15:59.612][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:15:59.613][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:15:59.614][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:15:59.615][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:15:59.616][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:15:59.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:15:59.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:15:59.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:15:59.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:15:59.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:15:59.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:15:59.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:15:59.635][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-01-10 20:15:59.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:15:59.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:15:59.640][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-01-10 20:16:00.022][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-01-10 20:16:00.382][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:00.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-01-10 20:16:00.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-01-10 20:16:00.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-01-10 20:16:00.393][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:00.394][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:00.395][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:00.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:00.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:00.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:00.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:00.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:00.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:00.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:00.410][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.413][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.419][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:00.420][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:00.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.422][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.424][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:00.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:00.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.428][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:00.429][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:00.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.431][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:00.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:00.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.440][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:00.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:00.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.445][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:00.446][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:00.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.448][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:00.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.454][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:00.455][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:00.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.457][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.458][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:00.459][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.461][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:00.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:00.477][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:00.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.479][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:00.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.485][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:00.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:00.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.487][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:00.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:00.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.493][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:00.494][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:00.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.497][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:00.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:00.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.501][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:00.502][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:00.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.503][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.505][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:00.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:00.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:00.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:00.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:00.551][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-01-10 20:16:00.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:00.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:00.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:00.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:00.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:00.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:00.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:00.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:00.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:00.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:00.591][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-01-10 20:16:00.592][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:00.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-01-10 20:16:00.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:00.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:00.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:00.597][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:00.598][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:00.599][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:00.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:00.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:00.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:00.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:00.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:00.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:00.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:00.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-01-10 20:16:00.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:00.615][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:00.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-01-10 20:16:00.968][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-01-10 20:16:01.342][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:01.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-01-10 20:16:01.347][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-01-10 20:16:01.350][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-01-10 20:16:01.352][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:01.353][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:01.354][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:01.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:01.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:01.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:01.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:01.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:01.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:01.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:01.368][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.369][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.371][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.376][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:01.378][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:01.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.380][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.381][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:01.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:01.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.385][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:01.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:01.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.388][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.390][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:01.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:01.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:01.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.397][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:01.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:01.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:01.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:01.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.415][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:01.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:01.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.420][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:01.421][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:01.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.423][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.424][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:01.425][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.427][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.428][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:01.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.432][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:01.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:01.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.435][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:01.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:01.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.440][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:01.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:01.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.443][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:01.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:01.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:01.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:01.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.455][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:01.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:01.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.463][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:01.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:01.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.467][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:01.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:01.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:01.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:01.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:01.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:01.688][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-01-10 20:16:01.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:01.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:01.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:01.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:01.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:01.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:01.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:01.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:01.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:01.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:01.709][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[2025-01-10 20:16:01.710][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-01-10 20:16:01.711][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:01.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-01-10 20:16:01.714][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:01.715][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:01.716][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:01.717][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:01.718][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:01.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:01.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:01.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:01.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:01.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:01.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:01.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:01.730][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[2025-01-10 20:16:01.731][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-01-10 20:16:01.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:01.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:01.736][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-01-10 20:16:02.120][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-01-10 20:16:02.482][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:02.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-01-10 20:16:02.495][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-01-10 20:16:02.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-01-10 20:16:02.504][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:02.507][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:02.510][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:02.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:02.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:02.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:02.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:02.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:02.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:02.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:02.535][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.539][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.547][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:02.548][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:02.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.550][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.557][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:02.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:02.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.560][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:02.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:02.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.566][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:02.567][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:02.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.569][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:02.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:02.575][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:02.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.577][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:02.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:02.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.583][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:02.584][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:02.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.586][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.588][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:02.589][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.591][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.592][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:02.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.597][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:02.598][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:02.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.600][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:02.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.606][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:02.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:02.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.609][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:02.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:02.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.615][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:02.616][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:02.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.618][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:02.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:02.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.624][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:02.625][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:02.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.627][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:02.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:02.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:02.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:02.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:02.677][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-01-10 20:16:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:02.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:02.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:02.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:02.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:02.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:02.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:02.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:02.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:02.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:02.702][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[2025-01-10 20:16:02.703][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-01-10 20:16:02.704][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:02.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-01-10 20:16:02.707][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:02.709][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:02.710][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:02.711][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:02.712][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:02.713][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:02.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:02.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:02.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:02.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:02.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:02.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:02.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:02.728][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-01-10 20:16:02.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:02.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:02.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-01-10 20:16:03.085][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-01-10 20:16:03.432][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:03.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-01-10 20:16:03.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-01-10 20:16:03.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-01-10 20:16:03.457][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:03.460][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:03.463][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:03.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:03.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:03.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:03.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:03.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:03.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:03.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:03.492][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.494][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.497][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.505][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:03.506][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:03.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.509][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.511][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:03.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:03.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.516][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:03.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:03.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.519][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:03.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:03.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:03.526][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:03.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.528][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:03.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:03.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.534][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:03.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:03.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:03.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.543][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:03.544][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:03.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.546][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.548][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:03.549][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.551][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.552][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:03.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.556][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:03.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:03.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.559][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:03.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.565][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:03.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:03.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.568][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:03.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:03.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.585][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:03.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:03.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.588][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:03.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:03.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.593][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:03.594][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:03.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.595][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:03.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:03.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:03.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:03.637][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-01-10 20:16:03.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:03.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:03.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:03.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:03.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:03.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:03.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:03.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:03.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:03.658][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-01-10 20:16:03.659][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:03.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-01-10 20:16:03.662][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:03.663][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:03.664][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:03.665][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:03.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:03.667][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:03.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:03.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:03.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:03.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:03.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:03.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:03.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:03.679][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-01-10 20:16:03.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:03.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:03.684][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-01-10 20:16:04.035][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-01-10 20:16:04.395][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:04.400][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-01-10 20:16:04.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-01-10 20:16:04.413][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-01-10 20:16:04.416][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:04.419][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:04.421][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:04.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.447][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.452][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.460][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:04.461][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:04.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.464][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.466][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:04.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:04.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.473][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:04.476][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:04.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.480][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:04.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:04.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.489][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:04.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:04.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:04.495][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:04.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:04.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:04.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:04.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.504][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.505][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:04.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.508][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.513][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:04.514][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:04.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.516][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:04.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:04.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.521][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:04.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:04.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.524][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:04.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:04.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.529][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:04.530][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:04.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.532][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.533][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:04.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:04.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:04.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.540][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.541][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:04.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:04.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:04.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:04.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.583][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-01-10 20:16:04.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.610][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[2025-01-10 20:16:04.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:04.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:16:04.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:04.617][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-10 20:16:04.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.688][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.TRACE[2025-01-10 20:16:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.852][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[2025-01-10 20:16:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.873][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.TRACE[2025-01-10 20:16:04.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.916][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.TRACE[2025-01-10 20:16:04.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.937][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.TRACE[2025-01-10 20:16:04.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.959][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[2025-01-10 20:16:04.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:04.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:04.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:04.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:04.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:04.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:04.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:04.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:04.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:04.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:04.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:05.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:05.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:05.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:05.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:05.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:05.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:05.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:05.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:05.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:05.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:05.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:05.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:05.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:05.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:05.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:05.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:05.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:05.048][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.TRACE[2025-01-10 20:16:05.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:05.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:05.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:05.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:05.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:05.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:05.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:05.069][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.TRACE[2025-01-10 20:16:05.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:05.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:05.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:05.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:05.136][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:05.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:05.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:05.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:05.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:05.844][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:05.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-01-10 20:16:05.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-01-10 20:16:05.863][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:05.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:05.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:05.875][private$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[2025-01-10 20:16:06.235][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[2025-01-10 20:16:06.603][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:06.607][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-01-10 20:16:06.616][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-01-10 20:16:06.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:06.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:06.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:06.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:06.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:06.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:06.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:06.645][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-01-10 20:16:06.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:06.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-01-10 20:16:06.652][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:06.654][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:06.656][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:06.658][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:06.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:06.661][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:06.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:06.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:06.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:06.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:06.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:06.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:06.677][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[2025-01-10 20:16:06.678][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-01-10 20:16:06.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:06.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:06.684][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-01-10 20:16:07.032][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-01-10 20:16:07.411][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:07.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-01-10 20:16:07.419][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-01-10 20:16:07.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-01-10 20:16:07.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:07.428][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:07.430][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:07.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:07.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:07.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:07.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:07.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:07.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:07.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:07.449][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.451][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.453][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.461][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:07.463][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:07.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.465][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.467][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:07.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.473][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:07.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:07.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.478][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:07.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:07.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:07.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:07.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.490][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:07.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:07.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.498][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:07.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:07.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.502][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:07.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:07.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.510][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:07.512][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:07.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.514][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:07.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.522][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:07.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:07.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.526][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.528][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:07.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:07.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.534][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.537][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.542][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:07.543][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:07.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.545][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:07.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:07.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.550][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:07.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:07.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.553][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:07.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:07.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:07.559][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:07.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.561][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.562][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:07.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:07.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:07.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:07.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:07.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:07.605][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-01-10 20:16:07.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:07.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:07.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:07.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:07.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:07.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:07.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:07.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:07.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:07.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:07.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:07.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:07.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:07.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:07.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:07.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:07.660][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[2025-01-10 20:16:07.661][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-01-10 20:16:07.662][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:07.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-01-10 20:16:07.665][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:07.666][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:07.667][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:07.668][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:07.669][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:07.670][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:07.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:07.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:07.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:07.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:07.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:07.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:07.681][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[2025-01-10 20:16:07.682][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-01-10 20:16:07.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:07.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:07.687][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-01-10 20:16:08.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-01-10 20:16:08.417][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:08.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-01-10 20:16:08.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-01-10 20:16:08.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-01-10 20:16:08.428][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:08.429][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:08.430][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:08.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.443][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.444][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.446][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.451][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:08.452][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:08.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.454][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.459][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:08.460][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:08.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.461][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:08.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.466][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:08.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:08.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.469][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:08.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:08.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.474][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:08.475][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:08.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.477][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:08.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:08.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.482][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:08.483][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:08.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.484][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.486][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:08.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:08.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.488][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.490][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:08.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:08.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.493][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.501][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:08.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:08.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.504][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.509][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:08.510][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:08.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.512][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.513][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:08.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.517][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:08.518][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:08.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.519][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:08.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:08.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:08.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:08.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.561][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-01-10 20:16:08.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.589][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[2025-01-10 20:16:08.592][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:08.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:16:08.594][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:08.596][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-10 20:16:08.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.627][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[2025-01-10 20:16:08.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.824][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[2025-01-10 20:16:08.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:08.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:08.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:08.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:08.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:08.982][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[2025-01-10 20:16:08.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:08.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:08.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:08.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:08.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:08.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:08.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.003][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[2025-01-10 20:16:09.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.049][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.TRACE[2025-01-10 20:16:09.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.077][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[2025-01-10 20:16:09.080][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:09.081][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-01-10 20:16:09.083][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:09.084][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-01-10 20:16:09.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.397][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.TRACE[2025-01-10 20:16:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.525][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[2025-01-10 20:16:09.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.551][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:09.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:09.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:16:09.562][biodb::testThat]
biodb.INFO [2025-01-10 20:16:09.563][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-01-10 20:16:09.564][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:09.565][biodb::testThat]
biodb.TRACE[2025-01-10 20:16:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-10 20:16:09.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-10 20:16:09.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:09.609][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[2025-01-10 20:16:09.613][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:09.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-10 20:16:09.615][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:09.616][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-10 20:16:09.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.627][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[2025-01-10 20:16:09.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.640][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[2025-01-10 20:16:09.643][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:09.645][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-10 20:16:09.646][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:09.647][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-10 20:16:09.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:09.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.692][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:09.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.712][private$selectFields]
biodb.TRACE[2025-01-10 20:16:09.713][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:09.713][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:09.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.718][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.722][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.723][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.724][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.725][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.726][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.728][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:09.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.757][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-10 20:16:09.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.778][private$selectFields]
biodb.TRACE[2025-01-10 20:16:09.779][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:09.780][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:09.780][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.785][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.787][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.788][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.790][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.791][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.792][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.794][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.795][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:09.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.808][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:09.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:09.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.827][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.828][private$selectFields]
biodb.TRACE[2025-01-10 20:16:09.829][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:09.830][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:09.831][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.835][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.836][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.837][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.839][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.841][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:09.842][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.843][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.845][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.846][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:09.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:09.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-10 20:16:09.860][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:09.861][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:09.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:09.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:09.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:09.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:09.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:09.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:09.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:09.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:09.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:09.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:09.950][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[2025-01-10 20:16:09.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:09.954][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:09.956][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:10.306][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:10.654][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:10.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-01-10 20:16:10.693][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-01-10 20:16:10.705][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:10.711][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:10.713][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:10.716][private$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[2025-01-10 20:16:11.087][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[2025-01-10 20:16:11.453][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:11.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-01-10 20:16:11.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-01-10 20:16:11.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.499][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.TRACE[2025-01-10 20:16:11.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:11.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.620][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:11.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.665][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.666][private$selectFields]
biodb.TRACE[2025-01-10 20:16:11.667][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:11.668][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:11.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.673][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.675][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.677][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.678][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.679][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.683][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.684][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:11.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.697][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-10 20:16:11.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.755][private$selectFields]
biodb.TRACE[2025-01-10 20:16:11.756][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:11.757][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:11.758][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.759][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.761][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.762][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.764][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.765][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.768][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.779][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.780][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.783][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.784][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:11.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.798][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:11.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.818][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.819][private$selectFields]
biodb.TRACE[2025-01-10 20:16:11.820][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:11.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:11.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.827][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.829][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.831][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.832][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.833][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:11.834][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.837][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.838][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:11.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.851][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-10 20:16:11.852][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:11.853][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:11.861][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:11.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:16:11.868][biodb::testThat]
biodb.INFO [2025-01-10 20:16:11.869][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-01-10 20:16:11.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:11.871][biodb::testThat]
biodb.TRACE[2025-01-10 20:16:11.874][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-10 20:16:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-10 20:16:11.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:11.906][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[2025-01-10 20:16:11.909][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:11.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-10 20:16:11.912][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:11.913][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-10 20:16:11.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.938][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[2025-01-10 20:16:11.941][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:11.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-10 20:16:11.943][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:11.945][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-10 20:16:11.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:11.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:11.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:11.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:11.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:11.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:11.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:11.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:11.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:11.996][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:11.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:11.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:11.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.006][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.TRACE[2025-01-10 20:16:12.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.015][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.016][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.017][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.019][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.020][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.022][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.024][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.025][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.027][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.031][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.032][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.044][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-10 20:16:12.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.063][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.064][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.065][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.066][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.067][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.071][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.073][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.074][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.075][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.076][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.077][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.078][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.080][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.081][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.094][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:12.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.113][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.114][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.115][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.116][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.118][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.120][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.123][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.124][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.125][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.129][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.130][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.142][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-10 20:16:12.143][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:12.144][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:12.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.179][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[2025-01-10 20:16:12.181][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[2025-01-10 20:16:12.184][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-10 20:16:12.187][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.188][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-10 20:16:12.191][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[2025-01-10 20:16:12.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-10 20:16:12.196][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.198][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-10 20:16:12.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.265][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:12.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.285][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.286][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.287][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.292][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.293][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.301][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.302][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.303][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.304][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.307][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-10 20:16:12.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.339][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.340][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.341][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.342][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.343][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.346][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.348][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.349][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.351][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.355][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.356][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:12.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.378][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.TRACE[2025-01-10 20:16:12.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.387][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.388][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.389][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.390][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.393][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.397][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.399][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.401][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.402][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.403][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.416][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-10 20:16:12.417][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:12.418][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:12.426][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:12.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:12.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:16:12.432][biodb::testThat]
biodb.INFO [2025-01-10 20:16:12.433][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-01-10 20:16:12.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:12.435][biodb::testThat]
biodb.TRACE[2025-01-10 20:16:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-10 20:16:12.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-10 20:16:12.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:12.472][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[2025-01-10 20:16:12.475][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-01-10 20:16:12.477][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.478][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-01-10 20:16:12.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.489][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.TRACE[2025-01-10 20:16:12.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.502][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[2025-01-10 20:16:12.505][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.506][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-01-10 20:16:12.507][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.509][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-01-10 20:16:12.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:12.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.553][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:12.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.572][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.573][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.574][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.575][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.580][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.583][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.585][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.586][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.589][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.590][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.603][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-01-10 20:16:12.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.622][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.623][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.624][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.625][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.629][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.630][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.631][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.633][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.634][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.635][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.640][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.642][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.644][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.645][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.657][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:12.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.676][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.683][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.684][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.685][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.686][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.687][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.688][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.689][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.692][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.693][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.705][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-01-10 20:16:12.706][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:12.707][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:12.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:12.753][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[2025-01-10 20:16:12.756][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.757][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-01-10 20:16:12.759][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.760][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-01-10 20:16:12.763][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[2025-01-10 20:16:12.766][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:12.767][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-01-10 20:16:12.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:12.769][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-01-10 20:16:12.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:12.836][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-01-10 20:16:12.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.854][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.855][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.856][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.857][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.858][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.862][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.863][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.865][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.866][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.867][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.868][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.871][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.872][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.884][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-01-10 20:16:12.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.903][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.904][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.905][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.906][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.908][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.910][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.913][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.915][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.919][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.920][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.932][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-01-10 20:16:12.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:12.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:12.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:12.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:12.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:12.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:12.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:12.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.951][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.951][private$selectFields]
biodb.TRACE[2025-01-10 20:16:12.952][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-01-10 20:16:12.953][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-01-10 20:16:12.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.955][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.962][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.963][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-01-10 20:16:12.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.965][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.967][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.968][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-01-10 20:16:12.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:12.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:12.987][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-01-10 20:16:12.988][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-01-10 20:16:12.989][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-01-10 20:16:13.006][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:13.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-01-10 20:16:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-10 20:16:13.013][biodb::testThat]
biodb.INFO [2025-01-10 20:16:13.014][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-01-10 20:16:13.015][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:13.016][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:13.018][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-01-10 20:16:13.019][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:13.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-01-10 20:16:13.021][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:13.022][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:13.023][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:13.024][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:13.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:13.026][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:13.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:13.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:13.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:13.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:13.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:13.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:13.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:13.039][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-01-10 20:16:13.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:13.042][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:13.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-01-10 20:16:13.391][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-01-10 20:16:13.746][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:13.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-01-10 20:16:13.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-01-10 20:16:13.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-01-10 20:16:13.766][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:13.769][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:13.772][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:13.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:13.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:13.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:13.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:13.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:13.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:13.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:13.798][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.800][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.803][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.811][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:13.812][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:13.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.815][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.816][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:13.818][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:13.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.820][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.822][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:13.823][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:13.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.825][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:13.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:13.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.830][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.831][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:13.832][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:13.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.834][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.835][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:13.836][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:13.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.839][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:13.840][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:13.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.842][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.843][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:13.844][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:13.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.846][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.847][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:13.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:13.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.850][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.851][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:13.852][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:13.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.853][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:13.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:13.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:13.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:13.892][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-01-10 20:16:13.893][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-01-10 20:16:13.900][biodb::testThat]
biodb.INFO [2025-01-10 20:16:13.901][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-01-10 20:16:13.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:13.902][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:13.910][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-01-10 20:16:13.912][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-01-10 20:16:13.913][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-01-10 20:16:13.914][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-01-10 20:16:13.915][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-01-10 20:16:13.916][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:13.917][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:13.918][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:13.919][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:13.920][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:13.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:13.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:13.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:13.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:13.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:13.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:13.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:13.933][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-01-10 20:16:13.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:13.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:13.938][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-01-10 20:16:14.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-01-10 20:16:14.644][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:14.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-01-10 20:16:14.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-01-10 20:16:14.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:14.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:14.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:14.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:14.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:14.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:14.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:14.683][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-01-10 20:16:14.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:14.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:14.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-01-10 20:16:15.041][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-01-10 20:16:15.407][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:15.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-01-10 20:16:15.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-01-10 20:16:15.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:15.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:15.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:15.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:15.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:15.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:15.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:15.447][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-01-10 20:16:15.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:15.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:15.457][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-01-10 20:16:15.811][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-01-10 20:16:16.165][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:16.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-01-10 20:16:16.174][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-01-10 20:16:16.178][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-01-10 20:16:16.181][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:16.183][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-01-10 20:16:16.185][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:16.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:16.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:16.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:16.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:16.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:16.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:16.202][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.TRACE[2025-01-10 20:16:16.205][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.210][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.218][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:16.220][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:16.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.223][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.225][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:16.227][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:16.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.230][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.232][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:16.234][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:16.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.237][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.240][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.243][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.245][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.247][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.250][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.252][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:16.253][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:16.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.258][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.259][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.261][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:16.262][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:16.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.263][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.281][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:16.283][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:16.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.284][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:16.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:16.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.288][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:16.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:16.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:16.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:16.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:16.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:16.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:16.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:16.326][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.327][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.329][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.334][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:16.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:16.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.337][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:16.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:16.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.342][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:16.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:16.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.345][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:16.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:16.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.350][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:16.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:16.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.353][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:16.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:16.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.360][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.365][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.366][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.368][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.373][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:16.374][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:16.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.376][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.377][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:16.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:16.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.381][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.382][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.384][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.389][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:16.390][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:16.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.392][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:16.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:16.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.397][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:16.398][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:16.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.400][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:16.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:16.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.405][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:16.406][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:16.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.408][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:16.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:16.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:16.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:16.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:16.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:16.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:16.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:16.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:16.451][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.452][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.454][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.459][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:16.460][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:16.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.461][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.463][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:16.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:16.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.467][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:16.468][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:16.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.469][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:16.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:16.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.475][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:16.476][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:16.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.477][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:16.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:16.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.484][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.486][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:16.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.492][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.494][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.495][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.499][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:16.500][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:16.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.501][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.503][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:16.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:16.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.507][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.508][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.509][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:16.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.515][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:16.516][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:16.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.517][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:16.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:16.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.523][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:16.524][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:16.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.525][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.527][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:16.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:16.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.531][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:16.532][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:16.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.533][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:16.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:16.600][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-01-10 20:16:16.601][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-01-10 20:16:16.602][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-01-10 20:16:16.614][biodb::testThat]
biodb.INFO [2025-01-10 20:16:16.615][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-01-10 20:16:16.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:16.630][biodb::testThat]
biodb.INFO [2025-01-10 20:16:16.661][biodb::testThat]
biodb.INFO [2025-01-10 20:16:16.662][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-01-10 20:16:16.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:16.664][biodb::testThat]
biodb.INFO [2025-01-10 20:16:16.672][biodb::testThat]
biodb.INFO [2025-01-10 20:16:16.674][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-01-10 20:16:16.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:16.676][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:16.679][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[2025-01-10 20:16:16.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:16.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:16.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:17.174][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:17.697][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:17.700][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-01-10 20:16:17.704][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-01-10 20:16:17.717][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:17.719][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:17.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:17.721][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:17.722][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:17.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:17.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:17.725][ef$get] fields variable is a list.
biodb.INFO [2025-01-10 20:16:17.727][biodb::testThat]
biodb.INFO [2025-01-10 20:16:17.728][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-01-10 20:16:17.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:17.730][biodb::testThat]
biodb.ERROR[2025-01-10 20:16:17.746][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-01-10 20:16:17.767][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-01-10 20:16:17.783][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-10 20:16:17.785][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-10 20:16:17.786][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-10 20:16:17.787][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-10 20:16:17.788][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:17.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:17.790][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:17.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:17.791][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-10 20:16:17.803][biodb::testContext]
biodb.INFO [2025-01-10 20:16:17.804][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:17.805][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-01-10 20:16:17.806][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:17.807][biodb::testContext]
biodb.INFO [2025-01-10 20:16:17.810][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:17.812][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:17.816][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:17.817][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-10 20:16:17.818][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.822][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-10 20:16:17.823][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.827][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-10 20:16:17.828][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.832][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-10 20:16:17.833][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-10 20:16:17.834][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-10 20:16:17.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.838][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-10 20:16:17.840][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-10 20:16:17.841][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.845][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-10 20:16:17.846][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-10 20:16:17.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.849][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-10 20:16:17.851][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-10 20:16:17.852][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-10 20:16:17.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.856][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-10 20:16:17.857][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.861][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-10 20:16:17.862][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-10 20:16:17.863][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-10 20:16:17.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.867][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:17.868][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-10 20:16:17.869][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-10 20:16:17.870][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-10 20:16:17.871][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-10 20:16:17.872][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-10 20:16:17.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.876][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-10 20:16:17.877][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-10 20:16:17.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.880][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-10 20:16:17.882][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-10 20:16:17.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.885][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-10 20:16:17.886][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-10 20:16:17.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.889][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[2025-01-10 20:16:17.890][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-10 20:16:17.891][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-10 20:16:17.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.895][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-10 20:16:17.897][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-10 20:16:17.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.900][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:17.901][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-10 20:16:17.905][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-10 20:16:17.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.909][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-10 20:16:17.910][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-10 20:16:17.911][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-10 20:16:17.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:17.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:17.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:17.915][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-10 20:16:17.917][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.918][self$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[2025-01-10 20:16:17.919][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.921][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:17.922][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.923][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.925][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.926][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:17.927][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:17.928][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.929][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-10 20:16:17.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:17.931][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.932][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.933][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:17.933][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:17.933][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:17.933][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:17.933][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:17.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:17.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:17.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:17.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:17.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:17.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:17.940][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.941][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.942][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:17.943][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:17.944][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.945][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.947][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-10 20:16:17.949][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.950][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:17.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:17.953][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.954][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.955][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.957][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:17.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:17.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.960][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-10 20:16:17.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:17.962][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.963][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:17.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:17.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:17.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:17.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:17.966][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:17.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:17.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:17.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:17.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:17.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:17.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.973][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:17.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:17.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.977][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.978][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-10 20:16:17.980][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.981][self$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[2025-01-10 20:16:17.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:17.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.988][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:17.989][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:17.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:17.991][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:17.992][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-10 20:16:17.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:17.994][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.995][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:17.996][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:17.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:17.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:17.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:18.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:18.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.004][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:18.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:18.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.008][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.009][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-10 20:16:18.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:18.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:18.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.020][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:18.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:18.036][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.038][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-10 20:16:18.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:18.040][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.040][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.041][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.042][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:18.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:18.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:18.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:18.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.049][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:18.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:18.051][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.052][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:18.054][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:18.055][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.060][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[2025-01-10 20:16:18.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.064][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.DEBUG[2025-01-10 20:16:18.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.073][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[2025-01-10 20:16:18.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.077][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[2025-01-10 20:16:18.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.081][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[2025-01-10 20:16:18.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.107][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[2025-01-10 20:16:18.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.129][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-10 20:16:18.131][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-10 20:16:18.132][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-10 20:16:18.134][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-10 20:16:18.135][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:18.136][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-10 20:16:18.138][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:18.139][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:18.140][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-10 20:16:18.142][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-10 20:16:18.143][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:18.144][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-10 20:16:18.146][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:18.147][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:18.149][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-10 20:16:18.150][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-10 20:16:18.151][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-10 20:16:18.153][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-10 20:16:18.154][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:18.155][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-10 20:16:18.157][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-10 20:16:18.158][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-10 20:16:18.159][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-10 20:16:18.160][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-10 20:16:18.162][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-10 20:16:18.163][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-10 20:16:18.164][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-10 20:16:18.166][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-10 20:16:18.167][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-10 20:16:18.168][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-10 20:16:18.170][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-10 20:16:18.171][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-10 20:16:18.172][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-10 20:16:18.173][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-10 20:16:18.175][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-10 20:16:18.176][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-10 20:16:18.177][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-10 20:16:18.179][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-10 20:16:18.180][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-10 20:16:18.181][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-10 20:16:18.183][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-10 20:16:18.184][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-10 20:16:18.185][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-10 20:16:18.187][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-10 20:16:18.188][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-10 20:16:18.189][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-10 20:16:18.191][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-10 20:16:18.192][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-10 20:16:18.193][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-10 20:16:18.194][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-10 20:16:18.196][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-10 20:16:18.197][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-10 20:16:18.198][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-10 20:16:18.200][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-10 20:16:18.201][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-10 20:16:18.202][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-10 20:16:18.204][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-10 20:16:18.205][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-10 20:16:18.206][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-10 20:16:18.207][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-10 20:16:18.209][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-10 20:16:18.210][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-10 20:16:18.211][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-10 20:16:18.213][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-10 20:16:18.214][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-10 20:16:18.215][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-10 20:16:18.216][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:18.218][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:18.219][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-10 20:16:18.220][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-10 20:16:18.222][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-10 20:16:18.223][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-10 20:16:18.224][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-10 20:16:18.226][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-10 20:16:18.227][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-10 20:16:18.228][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-10 20:16:18.229][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-10 20:16:18.231][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-10 20:16:18.232][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-10 20:16:18.233][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-10 20:16:18.235][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-10 20:16:18.236][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-10 20:16:18.237][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-10 20:16:18.239][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-10 20:16:18.240][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:18.241][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:18.242][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.244][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.244][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[2025-01-10 20:16:18.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.251][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[2025-01-10 20:16:18.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.257][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[2025-01-10 20:16:18.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.310][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[2025-01-10 20:16:18.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.316][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[2025-01-10 20:16:18.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.333][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[2025-01-10 20:16:18.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.339][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[2025-01-10 20:16:18.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:18.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:18.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:18.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:18.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:18.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:18.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:18.347][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:18.348][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-10 20:16:18.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.351][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:18.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.361][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.362][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-10 20:16:18.363][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-10 20:16:18.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:18.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.366][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-10 20:16:18.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-10 20:16:18.368][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-10 20:16:18.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:18.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:18.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:18.370][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:18.370][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-10 20:16:18.371][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:18.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.373][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:18.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:18.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:18.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:18.376][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:18.376][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-10 20:16:18.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:18.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:18.379][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:18.380][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-10 20:16:18.380][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-10 20:16:18.381][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:18.383][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:18.384][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-10 20:16:18.385][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:18.387][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:18.388][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:18.391][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-10 20:16:18.392][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-10 20:16:18.393][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-10 20:16:18.395][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-10 20:16:18.396][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:18.397][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:18.398][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-10 20:16:18.399][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-10 20:16:18.400][biodb::testThat]
biodb.INFO [2025-01-10 20:16:18.401][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-01-10 20:16:18.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:18.403][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:18.406][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-10 20:16:18.410][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:18.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:18.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-01-10 20:16:18.752][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-01-10 20:16:19.242][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:19.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-01-10 20:16:19.247][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-01-10 20:16:19.251][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[2025-01-10 20:16:19.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:19.254][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:19.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:19.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:19.949][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:19.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-01-10 20:16:19.958][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-01-10 20:16:19.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:19.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:19.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:19.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:19.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:19.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:19.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:19.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:19.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:19.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:19.987][private$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[2025-01-10 20:16:20.334][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[2025-01-10 20:16:20.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:20.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-01-10 20:16:20.720][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-01-10 20:16:20.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.789][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[2025-01-10 20:16:20.792][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:20.794][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-10 20:16:20.795][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:20.796][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-10 20:16:20.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.807][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[2025-01-10 20:16:20.809][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[2025-01-10 20:16:20.812][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:20.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-10 20:16:20.814][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:20.815][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-10 20:16:20.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.840][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[2025-01-10 20:16:20.843][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:20.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-01-10 20:16:20.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:20.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-01-10 20:16:20.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.859][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[2025-01-10 20:16:20.862][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:20.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-01-10 20:16:20.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:20.866][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-01-10 20:16:20.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:20.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:20.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:20.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:20.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:20.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:20.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:20.878][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[2025-01-10 20:16:20.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:20.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:20.884][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:21.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:21.573][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:21.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-01-10 20:16:21.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-01-10 20:16:21.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:21.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:21.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:21.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:21.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:21.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:21.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-10 20:16:21.624][biodb::testThat]
biodb.INFO [2025-01-10 20:16:21.625][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-01-10 20:16:21.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:21.629][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:21.633][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:21.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:21.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:21.643][private$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[2025-01-10 20:16:21.997][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[2025-01-10 20:16:22.352][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:22.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-01-10 20:16:22.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-01-10 20:16:22.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:22.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:22.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:22.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:22.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:22.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:22.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:22.373][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[2025-01-10 20:16:22.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:22.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:22.379][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-01-10 20:16:22.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-01-10 20:16:23.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:23.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-01-10 20:16:23.100][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-01-10 20:16:23.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:23.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-10 20:16:23.116][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-10 20:16:23.118][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-10 20:16:23.119][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-10 20:16:23.120][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-10 20:16:23.120][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.128][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.148][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-10 20:16:23.152][biodb::testContext]
biodb.INFO [2025-01-10 20:16:23.153][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:23.154][biodb::testContext] Test context - Test web services
biodb.INFO [2025-01-10 20:16:23.155][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:23.156][biodb::testContext]
biodb.INFO [2025-01-10 20:16:23.158][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:23.160][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:23.163][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:23.164][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-10 20:16:23.165][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.169][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-10 20:16:23.170][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.173][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-10 20:16:23.174][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.177][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-10 20:16:23.178][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-10 20:16:23.179][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-10 20:16:23.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.183][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-10 20:16:23.184][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-10 20:16:23.185][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.188][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-10 20:16:23.189][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-10 20:16:23.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.193][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-10 20:16:23.194][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-10 20:16:23.195][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-10 20:16:23.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.198][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[2025-01-10 20:16:23.198][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-10 20:16:23.199][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.203][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-10 20:16:23.204][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-10 20:16:23.205][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-10 20:16:23.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.208][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:23.209][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-10 20:16:23.210][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-10 20:16:23.211][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-10 20:16:23.212][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-10 20:16:23.213][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-10 20:16:23.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.216][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-10 20:16:23.217][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-10 20:16:23.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.221][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-10 20:16:23.222][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-10 20:16:23.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.225][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-10 20:16:23.226][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-10 20:16:23.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.229][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-10 20:16:23.230][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-10 20:16:23.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.234][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-10 20:16:23.235][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-10 20:16:23.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.237][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[2025-01-10 20:16:23.238][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:23.239][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-10 20:16:23.242][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-10 20:16:23.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.246][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-10 20:16:23.247][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-10 20:16:23.248][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-10 20:16:23.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.251][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[2025-01-10 20:16:23.252][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-10 20:16:23.254][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.255][self$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[2025-01-10 20:16:23.256][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.257][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:23.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.261][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:23.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:23.263][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.264][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-10 20:16:23.265][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:23.266][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.267][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.268][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:23.268][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:23.268][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:23.268][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:23.268][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:23.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:23.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:23.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.276][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:23.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:23.278][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.279][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.280][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-10 20:16:23.282][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.283][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:23.284][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.285][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:23.286][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.288][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.289][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.290][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:23.291][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:23.292][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.293][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-10 20:16:23.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:23.294][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.295][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.296][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:23.296][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:23.296][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:23.296][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:23.296][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:23.297][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:23.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:23.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.304][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:23.305][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:23.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.307][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.308][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-10 20:16:23.310][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.311][self$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[2025-01-10 20:16:23.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:23.314][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.318][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:23.318][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:23.319][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.320][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-10 20:16:23.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:23.322][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.323][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.324][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:23.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:23.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.330][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.331][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.332][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:23.333][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:23.334][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.335][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.336][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-10 20:16:23.338][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.339][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:23.340][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:23.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.343][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.344][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.345][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:23.346][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:23.347][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.348][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-10 20:16:23.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:23.350][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.352][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.353][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:23.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.355][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:23.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.359][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:23.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:23.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.362][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:23.364][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:23.365][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.365][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[2025-01-10 20:16:23.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.378][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[2025-01-10 20:16:23.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.438][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-10 20:16:23.439][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-10 20:16:23.441][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-10 20:16:23.442][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-10 20:16:23.443][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:23.445][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-10 20:16:23.446][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:23.447][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:23.449][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-10 20:16:23.450][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-10 20:16:23.451][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:23.453][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-10 20:16:23.454][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:23.455][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:23.456][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-10 20:16:23.458][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-10 20:16:23.459][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-10 20:16:23.460][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-10 20:16:23.462][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:23.463][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-10 20:16:23.464][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-10 20:16:23.466][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-10 20:16:23.467][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-10 20:16:23.473][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-10 20:16:23.475][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-10 20:16:23.476][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-10 20:16:23.477][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-10 20:16:23.479][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-10 20:16:23.480][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-10 20:16:23.481][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-10 20:16:23.482][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-10 20:16:23.484][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-10 20:16:23.485][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-10 20:16:23.486][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-10 20:16:23.487][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-10 20:16:23.489][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-10 20:16:23.490][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-10 20:16:23.491][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-10 20:16:23.493][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-10 20:16:23.494][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-10 20:16:23.495][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-10 20:16:23.496][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-10 20:16:23.498][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-10 20:16:23.499][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-10 20:16:23.500][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-10 20:16:23.501][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-10 20:16:23.503][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-10 20:16:23.504][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-10 20:16:23.505][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-10 20:16:23.507][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-10 20:16:23.508][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-10 20:16:23.509][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-10 20:16:23.510][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-10 20:16:23.512][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-10 20:16:23.513][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-10 20:16:23.514][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-10 20:16:23.515][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-10 20:16:23.517][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-10 20:16:23.518][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-10 20:16:23.519][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-10 20:16:23.521][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-10 20:16:23.522][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-10 20:16:23.523][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-10 20:16:23.524][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-10 20:16:23.526][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-10 20:16:23.527][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-10 20:16:23.528][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:23.529][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:23.531][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-10 20:16:23.532][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-10 20:16:23.533][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-10 20:16:23.534][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-10 20:16:23.536][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-10 20:16:23.537][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-10 20:16:23.538][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-10 20:16:23.540][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-10 20:16:23.541][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-10 20:16:23.542][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-10 20:16:23.543][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-10 20:16:23.545][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-10 20:16:23.546][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-10 20:16:23.547][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-10 20:16:23.548][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-10 20:16:23.550][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-10 20:16:23.551][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:23.552][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:23.553][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.555][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.620][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[2025-01-10 20:16:23.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:23.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.649][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[2025-01-10 20:16:23.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:23.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:23.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:23.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:23.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:23.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:23.655][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[2025-01-10 20:16:23.656][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:23.658][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-10 20:16:23.660][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.661][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.662][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:23.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.665][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.666][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-10 20:16:23.667][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-10 20:16:23.668][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:23.669][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.670][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-10 20:16:23.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-10 20:16:23.672][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-10 20:16:23.673][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:23.674][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:23.674][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:23.674][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:23.675][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-10 20:16:23.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.678][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:23.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:23.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:23.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:23.681][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:23.681][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-10 20:16:23.682][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:23.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:23.684][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:23.685][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-10 20:16:23.685][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-10 20:16:23.686][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:23.687][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:23.689][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-10 20:16:23.690][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:23.692][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:23.693][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:23.696][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-10 20:16:23.697][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-10 20:16:23.698][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-10 20:16:23.700][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-10 20:16:23.701][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:23.702][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:23.703][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-10 20:16:23.704][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-10 20:16:23.705][biodb::testThat]
biodb.INFO [2025-01-10 20:16:23.706][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-01-10 20:16:23.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:23.708][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:23.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-10 20:16:23.714][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:23.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-10 20:16:23.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:23.718][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-10 20:16:23.721][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-01-10 20:16:23.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:23.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:23.727][private$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[2025-01-10 20:16:24.069][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[2025-01-10 20:16:24.419][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:24.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-01-10 20:16:24.425][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-01-10 20:16:24.433][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-10 20:16:24.434][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-10 20:16:24.435][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-10 20:16:24.436][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-10 20:16:24.437][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.438][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.440][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-10 20:16:24.444][biodb::testContext]
biodb.INFO [2025-01-10 20:16:24.445][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:24.446][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-01-10 20:16:24.447][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-10 20:16:24.448][biodb::testContext]
biodb.INFO [2025-01-10 20:16:24.450][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:24.452][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:24.456][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:24.457][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-10 20:16:24.458][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.461][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-10 20:16:24.462][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.466][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-10 20:16:24.467][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.470][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-10 20:16:24.471][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-10 20:16:24.472][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-10 20:16:24.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.476][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-10 20:16:24.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-10 20:16:24.478][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.490][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-10 20:16:24.492][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-10 20:16:24.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.494][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[2025-01-10 20:16:24.495][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-10 20:16:24.496][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-10 20:16:24.497][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-10 20:16:24.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.500][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-10 20:16:24.501][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.505][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-10 20:16:24.506][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-10 20:16:24.507][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-10 20:16:24.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.510][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:24.511][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-10 20:16:24.512][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-10 20:16:24.513][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-10 20:16:24.514][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-10 20:16:24.515][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-10 20:16:24.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.517][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[2025-01-10 20:16:24.518][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-10 20:16:24.519][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-10 20:16:24.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.522][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-10 20:16:24.523][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-10 20:16:24.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.526][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[2025-01-10 20:16:24.527][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-10 20:16:24.528][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-10 20:16:24.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.531][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-10 20:16:24.532][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-10 20:16:24.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.535][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[2025-01-10 20:16:24.536][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-10 20:16:24.537][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-10 20:16:24.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.540][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-10 20:16:24.541][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-10 20:16:24.544][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-10 20:16:24.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.546][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[2025-01-10 20:16:24.547][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-10 20:16:24.548][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-10 20:16:24.549][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-10 20:16:24.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.553][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-10 20:16:24.554][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.555][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-10 20:16:24.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.557][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:24.558][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.559][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.560][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.562][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:24.563][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:24.564][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.565][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-10 20:16:24.566][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:24.567][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.568][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:24.568][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:24.568][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:24.568][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:24.568][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:24.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:24.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:24.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.576][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:24.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:24.578][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.579][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.580][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-10 20:16:24.582][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.583][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:24.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:24.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.590][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:24.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:24.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.593][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-10 20:16:24.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:24.594][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:24.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:24.596][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:24.596][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-10 20:16:24.596][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-10 20:16:24.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:24.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:24.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.604][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:24.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:24.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.607][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.608][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-10 20:16:24.610][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.611][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-10 20:16:24.612][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.613][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:24.614][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.616][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.618][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-10 20:16:24.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:24.620][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.621][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-10 20:16:24.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:24.622][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.623][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.624][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.625][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:24.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:24.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.632][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:24.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:24.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.635][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.636][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-10 20:16:24.638][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.639][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-10 20:16:24.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.641][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:24.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.643][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.644][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.645][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-10 20:16:24.646][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:24.647][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.648][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-10 20:16:24.649][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:24.650][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.651][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:24.652][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.653][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-10 20:16:24.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:24.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:24.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:24.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:24.659][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.660][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:24.661][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:24.662][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:24.663][self$setPropertyValue]
biodb.DEBUG[2025-01-10 20:16:24.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:24.665][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.666][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[2025-01-10 20:16:24.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.674][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[2025-01-10 20:16:24.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.708][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[2025-01-10 20:16:24.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.729][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.DEBUG[2025-01-10 20:16:24.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.733][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.DEBUG[2025-01-10 20:16:24.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.738][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-10 20:16:24.740][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-10 20:16:24.741][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-10 20:16:24.742][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-10 20:16:24.743][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:24.745][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-10 20:16:24.746][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:24.747][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:24.749][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-10 20:16:24.750][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-10 20:16:24.751][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:24.753][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-10 20:16:24.754][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-10 20:16:24.755][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-10 20:16:24.757][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-10 20:16:24.758][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-10 20:16:24.759][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-10 20:16:24.760][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-10 20:16:24.762][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:24.763][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-10 20:16:24.764][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-10 20:16:24.766][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-10 20:16:24.767][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-10 20:16:24.768][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-10 20:16:24.770][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-10 20:16:24.771][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-10 20:16:24.772][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-10 20:16:24.774][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-10 20:16:24.775][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-10 20:16:24.776][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-10 20:16:24.778][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-10 20:16:24.779][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-10 20:16:24.780][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-10 20:16:24.782][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-10 20:16:24.783][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-10 20:16:24.784][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-10 20:16:24.786][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-10 20:16:24.787][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-10 20:16:24.788][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-10 20:16:24.789][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-10 20:16:24.791][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-10 20:16:24.792][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-10 20:16:24.793][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-10 20:16:24.795][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-10 20:16:24.796][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-10 20:16:24.797][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-10 20:16:24.799][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-10 20:16:24.800][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-10 20:16:24.801][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-10 20:16:24.808][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-10 20:16:24.809][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-10 20:16:24.810][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-10 20:16:24.812][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-10 20:16:24.813][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-10 20:16:24.814][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-10 20:16:24.815][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-10 20:16:24.817][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-10 20:16:24.818][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-10 20:16:24.819][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-10 20:16:24.821][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-10 20:16:24.822][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-10 20:16:24.823][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-10 20:16:24.824][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-10 20:16:24.826][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-10 20:16:24.827][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-10 20:16:24.828][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-10 20:16:24.829][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:24.831][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:24.832][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-10 20:16:24.833][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-10 20:16:24.835][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-10 20:16:24.836][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-10 20:16:24.837][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-10 20:16:24.838][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-10 20:16:24.840][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-10 20:16:24.841][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-10 20:16:24.842][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-10 20:16:24.844][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-10 20:16:24.845][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-10 20:16:24.846][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-10 20:16:24.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-10 20:16:24.849][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-10 20:16:24.850][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-10 20:16:24.851][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-10 20:16:24.853][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-10 20:16:24.854][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-10 20:16:24.856][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.858][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.860][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[2025-01-10 20:16:24.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.878][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[2025-01-10 20:16:24.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.933][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[2025-01-10 20:16:24.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.963][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[2025-01-10 20:16:24.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:24.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.982][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[2025-01-10 20:16:24.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:24.991][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[2025-01-10 20:16:24.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:24.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:24.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:24.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:24.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:24.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:25.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:25.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:25.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:25.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:25.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:25.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:25.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:25.010][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.DEBUG[2025-01-10 20:16:25.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-10 20:16:25.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:25.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:25.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:25.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:25.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:25.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:25.022][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-01-10 20:16:25.024][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-01-10 20:16:25.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:25.028][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-10 20:16:25.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:25.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-10 20:16:25.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:25.034][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-10 20:16:25.036][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:25.037][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-01-10 20:16:25.039][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-10 20:16:25.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-10 20:16:25.042][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:25.043][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-01-10 20:16:25.045][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-01-10 20:16:25.046][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-01-10 20:16:25.048][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-10 20:16:25.049][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-10 20:16:25.049][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-10 20:16:25.049][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-10 20:16:25.051][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-10 20:16:25.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:25.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:25.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-10 20:16:25.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-10 20:16:25.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-10 20:16:25.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-10 20:16:25.061][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:25.061][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-01-10 20:16:25.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-10 20:16:25.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-10 20:16:25.065][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-10 20:16:25.067][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-01-10 20:16:25.067][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-01-10 20:16:25.069][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-10 20:16:25.071][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-10 20:16:25.073][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-01-10 20:16:25.076][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-10 20:16:25.078][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-10 20:16:25.080][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-10 20:16:25.085][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-01-10 20:16:25.087][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-01-10 20:16:25.089][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-01-10 20:16:25.091][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-01-10 20:16:25.093][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:25.094][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-10 20:16:25.097][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-01-10 20:16:25.098][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-01-10 20:16:25.100][biodb::testThat]
biodb.INFO [2025-01-10 20:16:25.102][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-01-10 20:16:25.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-10 20:16:25.105][biodb::testThat]
biodb.DEBUG[2025-01-10 20:16:25.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-01-10 20:16:25.115][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:25.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-01-10 20:16:25.120][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:25.122][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-01-10 20:16:25.125][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[2025-01-10 20:16:25.128][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-10 20:16:25.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-01-10 20:16:25.131][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-10 20:16:25.132][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-01-10 20:16:25.136][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-01-10 20:16:25.137][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-01-10 20:16:25.139][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-01-10 20:16:25.140][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-01-10 20:16:25.141][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-10 20:16:25.142][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-01-10 20:16:25.143][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-01-10 20:16:25.144][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-10 20:16:25.145][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-10 20:16:25.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:25.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:25.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:25.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:25.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:25.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:25.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-10 20:16:25.158][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-01-10 20:16:25.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-10 20:16:25.161][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-10 20:16:25.163][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-01-10 20:16:25.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-01-10 20:16:26.523][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-10 20:16:26.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-01-10 20:16:26.529][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-01-10 20:16:26.531][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-01-10 20:16:26.533][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-10 20:16:26.534][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-01-10 20:16:26.535][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-01-10 20:16:26.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-10 20:16:26.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:26.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:26.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:26.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:26.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:26.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-10 20:16:26.549][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.551][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.552][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.569][ef$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:26.570][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:26.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.572][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-01-10 20:16:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-01-10 20:16:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.577][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:26.578][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:26.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.580][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-10 20:16:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-10 20:16:26.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.585][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-10 20:16:26.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-10 20:16:26.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.597][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.598][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-10 20:16:26.599][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-10 20:16:26.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.601][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.602][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:26.603][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:26.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.605][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-10 20:16:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.610][ef$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:26.611][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:26.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.613][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-01-10 20:16:26.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-10 20:16:26.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.618][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:26.619][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:26.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.620][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:26.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-10 20:16:26.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.625][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:26.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:26.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.628][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-10 20:16:26.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-10 20:16:26.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.633][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:26.634][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:26.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.636][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.637][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-01-10 20:16:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-01-10 20:16:26.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:26.642][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:26.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.644][ef$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-10 20:16:26.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-10 20:16:26.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-10 20:16:26.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-10 20:16:26.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-10 20:16:26.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-10 20:16:26.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-10 20:16:26.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-10 20:16:26.694][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-01-10 20:16:26.699][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-10 20:16:26.701][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-01-10 20:16:26.702][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-01-10 20:16:26.703][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-10 20:16:26.704][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-10 20:16:26.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-10 20:16:26.706][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-10 20:16:26.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-10 20:16:26.708][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-10 20:16:26.709][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
22.054 1.208 55.017
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.916 | 0.084 | 1.587 | |
| ChebiEntry | 0.155 | 0.002 | 0.156 | |