Pierrick Roger
| Snapshot Date: 2025-03-26 13:40 -0400 (Wed, 26 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-27 11:47 -0400 (Thu, 27 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 204/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2025-03-27 04:36:37 -0000 (Thu, 27 Mar 2025) |
| EndedAt: 2025-03-27 04:49:46 -0000 (Thu, 27 Mar 2025) |
| EllapsedTime: 789.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘biodbChebi’ ... ** this is package ‘biodbChebi’ version ‘1.13.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-03-27 04:37:51.388][biodb::testContext]
biodb.INFO [2025-03-27 04:37:51.391][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:37:51.397][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-27 04:37:51.399][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:37:51.404][biodb::testContext]
biodb.INFO [2025-03-27 04:37:51.422][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:37:51.429][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-27 04:37:51.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:37:51.452][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-27 04:37:51.454][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.468][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-27 04:37:51.528][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.542][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-27 04:37:51.543][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.552][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-27 04:37:51.554][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-27 04:37:51.556][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-27 04:37:51.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.570][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-27 04:37:51.572][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-27 04:37:51.577][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.587][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-27 04:37:51.593][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-27 04:37:51.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.603][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-27 04:37:51.609][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-27 04:37:51.611][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-27 04:37:51.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.625][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-27 04:37:51.627][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.641][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-27 04:37:51.642][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-27 04:37:51.644][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-27 04:37:51.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.662][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:37:51.664][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-27 04:37:51.670][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-27 04:37:51.671][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-27 04:37:51.677][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-27 04:37:51.678][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-27 04:37:51.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.684][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-27 04:37:51.694][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-27 04:37:51.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.699][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-27 04:37:51.705][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-27 04:37:51.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.719][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-27 04:37:51.725][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-27 04:37:51.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.735][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-27 04:37:51.737][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-27 04:37:51.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.745][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.DEBUG[2025-03-27 04:37:51.747][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-27 04:37:51.756][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-27 04:37:51.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.762][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:37:51.763][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-27 04:37:51.822][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-27 04:37:51.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.827][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-27 04:37:51.833][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-27 04:37:51.835][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-27 04:37:51.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:51.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:51.857][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-27 04:37:51.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.041][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-27 04:37:52.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.108][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:37:52.114][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.115][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.121][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.129][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:37:52.130][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:37:52.136][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.138][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-27 04:37:52.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:37:52.146][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.153][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.155][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:37:52.155][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:37:52.155][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:37:52.155][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:37:52.155][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:37:52.162][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:37:52.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.171][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:37:52.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.187][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:37:52.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:37:52.201][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.203][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.210][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-27 04:37:52.218][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.219][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:37:52.225][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.227][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:37:52.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.236][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.244][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:37:52.250][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:37:52.251][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.257][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-27 04:37:52.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:37:52.265][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.268][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:37:52.268][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:37:52.268][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:37:52.268][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:37:52.268][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:37:52.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:37:52.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:37:52.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.297][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:37:52.300][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:37:52.306][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.307][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.313][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-27 04:37:52.320][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.322][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-27 04:37:52.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.329][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:37:52.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.337][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.338][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:37:52.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:37:52.353][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.355][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-27 04:37:52.356][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:37:52.362][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.369][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:37:52.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.379][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:37:52.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.388][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.394][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.395][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:37:52.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:37:52.403][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.408][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.410][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-27 04:37:52.417][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:37:52.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:37:52.432][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.436][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.441][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.443][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:37:52.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:37:52.450][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.456][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-27 04:37:52.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:37:52.460][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.466][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:52.468][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:37:52.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:37:52.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:52.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:52.497][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:37:52.499][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:37:52.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:37:52.512][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:52.514][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:37:52.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:37:52.530][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.531][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.DEBUG[2025-03-27 04:37:52.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:52.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:52.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:52.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:52.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:52.815][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-27 04:37:52.830][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-27 04:37:52.832][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-27 04:37:52.839][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-27 04:37:52.845][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:37:52.847][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-27 04:37:52.854][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-27 04:37:52.856][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-27 04:37:52.863][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-27 04:37:52.869][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-27 04:37:52.872][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:37:52.878][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-27 04:37:52.885][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-27 04:37:52.887][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-27 04:37:52.894][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-27 04:37:52.900][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-27 04:37:52.903][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-27 04:37:52.909][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-27 04:37:52.912][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:37:52.918][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-27 04:37:52.925][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-27 04:37:52.927][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-27 04:37:52.933][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-27 04:37:52.936][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-27 04:37:52.942][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-27 04:37:52.948][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-27 04:37:52.951][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-27 04:37:52.957][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-27 04:37:52.959][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-27 04:37:52.966][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-27 04:37:52.968][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-27 04:37:52.974][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-27 04:37:52.980][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-27 04:37:52.983][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-27 04:37:52.989][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-27 04:37:52.991][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-27 04:37:52.998][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-27 04:37:53.000][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-27 04:37:53.006][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-27 04:37:53.012][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-27 04:37:53.015][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-27 04:37:53.021][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-27 04:37:53.023][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-27 04:37:53.030][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-27 04:37:53.036][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-27 04:37:53.039][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-27 04:37:53.061][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-27 04:37:53.063][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-27 04:37:53.070][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-27 04:37:53.072][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-27 04:37:53.078][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-27 04:37:53.084][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-27 04:37:53.086][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-27 04:37:53.093][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-27 04:37:53.095][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-27 04:37:53.101][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-27 04:37:53.104][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-27 04:37:53.106][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-27 04:37:53.108][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-27 04:37:53.114][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-27 04:37:53.120][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-27 04:37:53.123][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-27 04:37:53.129][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-27 04:37:53.131][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-27 04:37:53.137][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-27 04:37:53.139][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-27 04:37:53.146][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:37:53.148][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:37:53.154][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-27 04:37:53.161][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-27 04:37:53.163][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-27 04:37:53.169][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-27 04:37:53.171][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-27 04:37:53.178][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-27 04:37:53.180][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-27 04:37:53.186][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-27 04:37:53.192][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-27 04:37:53.195][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-27 04:37:53.201][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-27 04:37:53.203][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-27 04:37:53.209][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-27 04:37:53.212][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-27 04:37:53.218][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-27 04:37:53.235][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-27 04:37:53.242][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:37:53.251][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:37:53.252][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.259][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.292][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[2025-03-27 04:37:53.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.330][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.DEBUG[2025-03-27 04:37:53.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.443][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.DEBUG[2025-03-27 04:37:53.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:37:53.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:53.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:53.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:53.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:53.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:37:53.596][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-27 04:37:53.627][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-27 04:37:53.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:53.635][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-27 04:37:53.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:53.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:37:53.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:53.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:37:53.651][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:53.656][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-27 04:37:53.658][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-27 04:37:53.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:37:53.665][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:53.667][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-27 04:37:53.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-27 04:37:53.674][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-27 04:37:53.675][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-27 04:37:53.681][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:37:53.681][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:37:53.681][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:37:53.683][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-27 04:37:53.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:53.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:53.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:37:53.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:37:53.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:37:53.699][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:37:53.705][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:37:53.705][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-27 04:37:53.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:37:53.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:37:53.713][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-27 04:37:53.714][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-27 04:37:53.714][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-27 04:37:53.731][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:37:53.738][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:37:53.745][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-27 04:37:53.747][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:37:53.753][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:37:53.756][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:37:53.826][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-27 04:37:53.828][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-27 04:37:53.842][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-27 04:37:53.852][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-27 04:37:53.889][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:37:53.891][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:37:53.897][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-27 04:37:53.898][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-27 04:37:53.923][biodb::testThat]
biodb.INFO [2025-03-27 04:37:53.928][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-27 04:37:53.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:37:53.931][biodb::testThat]
biodb.TRACE[2025-03-27 04:37:53.949][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-27 04:37:53.952][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:37:53.965][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:37:53.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:37:53.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:53.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:54.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:54.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:54.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:54.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:37:54.062][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.126][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:54.128][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:54.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:54.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.239][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:54.244][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:54.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:54.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.268][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:54.270][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:54.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:54.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.294][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.320][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:54.326][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:54.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.333][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.335][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:54.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.350][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:37:54.351][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.365][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:37:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:54.382][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:54.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:54.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:54.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.406][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:54.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:54.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:54.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:54.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.431][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:37:54.437][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:54.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:37:54.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:54.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.461][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:54.463][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:54.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:54.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:54.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:54.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:37:54.801][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-27 04:37:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:54.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:54.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:54.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:54.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:37:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:37:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:37:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:37:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.974][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-27 04:37:54.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-27 04:37:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-27 04:37:54.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-27 04:37:54.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:54.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.232][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.238][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:55.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:55.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:55.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:55.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.423][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:55.424][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:55.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:55.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.485][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:55.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:55.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.495][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:55.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.509][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:55.511][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:55.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.518][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:55.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:55.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.600][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.606][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:55.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.686][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:55.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:55.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:55.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.774][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:55.776][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:55.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.783][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:55.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.822][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.836][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.847][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.861][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.871][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:55.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.909][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.934][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.950][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.957][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.959][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:55.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:55.996][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.021][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.047][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.062][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.150][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.152][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.240][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.247][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.287][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:56.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:56.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.311][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:56.317][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:56.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.335][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:56.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:56.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.358][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.364][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.383][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.388][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:56.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.407][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:56.413][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:56.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.431][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:56.437][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:56.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.440][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:56.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:56.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.479][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-27 04:37:56.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:56.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.502][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:56.508][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:56.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.526][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:56.528][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:56.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.535][ef$get] fields variable is a list.
biodb.INFO [2025-03-27 04:37:56.558][biodb::testThat]
biodb.INFO [2025-03-27 04:37:56.560][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-27 04:37:56.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:37:56.567][biodb::testThat]
biodb.DEBUG[2025-03-27 04:37:56.613][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-27 04:37:56.631][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:37:56.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-27 04:37:56.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:37:56.678][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-27 04:37:56.679][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:37:56.759][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:37:56.765][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:37:56.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:37:56.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:37:56.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:37:56.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:37:56.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:37:56.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:37:56.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:37:56.813][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:56.815][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:56.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:56.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:56.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.917][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:56.919][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:56.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.933][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:37:56.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:37:56.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.944][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:56.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:56.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.957][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.959][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:37:56.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:37:56.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.975][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.980][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:56.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:37:56.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:37:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:56.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.004][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:57.006][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:57.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:37:57.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:37:57.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.030][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:57.032][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:57.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.045][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:57.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:37:57.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.056][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:37:57.062][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:57.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.071][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:37:57.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:37:57.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:57.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:57.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:57.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:37:57.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.111][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.140][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:37:57.142][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:57.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:37:57.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:37:57.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.166][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:57.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:57.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:37:57.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:37:57.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:37:57.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:37:57.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:37:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:37:57.325][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-27 04:37:57.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-27 04:37:57.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-27 04:37:57.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-27 04:37:57.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-27 04:37:57.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-27 04:37:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-27 04:37:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:37:57.383][biodb::testThat]
biodb.INFO [2025-03-27 04:37:57.389][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-27 04:37:57.391][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:37:57.396][biodb::testThat]
biodb.TRACE[2025-03-27 04:37:57.405][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.414][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:37:57.416][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-27 04:37:57.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:37:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:37:57.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:37:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:37:57.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:37:57.543][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-27 04:37:57.558][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-27 04:37:57.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:37:57.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-27 04:37:57.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:37:57.718][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-27 04:37:57.792][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:37:57.805][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:37:57.806][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:37:57.813][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:37:59.243][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:38:00.539][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:38:00.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-27 04:38:00.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-27 04:38:00.686][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-27 04:38:00.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:00.857][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:00.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:00.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:00.862][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:00.864][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:00.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:00.872][ef$get] fields variable is a list.
biodb.INFO [2025-03-27 04:38:00.887][biodb::testThat]
biodb.INFO [2025-03-27 04:38:00.893][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-27 04:38:00.894][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:00.896][biodb::testThat]
biodb.TRACE[2025-03-27 04:38:00.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:00.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:00.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:01.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:01.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:01.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:01.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:01.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:38:01.264][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:38:01.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:38:01.268][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:38:01.270][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-27 04:38:01.342][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.343][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-27 04:38:01.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:01.351][biodb::testThat]
biodb.TRACE[2025-03-27 04:38:01.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:01.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:01.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:01.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:01.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-27 04:38:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-27 04:38:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-27 04:38:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-27 04:38:01.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:01.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:01.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:01.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:01.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:01.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.734][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-27 04:38:01.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.749][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-27 04:38:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-27 04:38:01.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:01.760][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-27 04:38:01.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-27 04:38:01.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:01.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:38:01.787][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.793][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-27 04:38:01.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:01.796][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.824][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.826][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-27 04:38:01.827][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:01.833][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.858][biodb::testThat]
biodb.INFO [2025-03-27 04:38:01.859][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-27 04:38:01.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:01.867][biodb::testThat]
biodb.DEBUG[2025-03-27 04:38:01.880][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-27 04:38:03.484][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-27 04:38:04.839][biodb::testThat]
biodb.INFO [2025-03-27 04:38:04.851][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-27 04:38:04.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:04.854][biodb::testThat]
biodb.DEBUG[2025-03-27 04:38:05.641][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-27 04:38:06.462][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:06.463][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:06.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:06.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:06.474][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:06.475][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:06.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:06.484][ef$get] fields variable is a list.
biodb.INFO [2025-03-27 04:38:06.487][biodb::testThat]
biodb.INFO [2025-03-27 04:38:06.488][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-27 04:38:06.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:38:06.497][biodb::testThat]
biodb.TRACE[2025-03-27 04:38:06.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:06.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:06.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:06.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:06.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:06.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:06.817][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:38:06.833][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:38:06.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:38:06.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:38:06.857][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-27 04:38:07.013][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:38:07.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:38:07.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:38:07.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:38:07.024][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-27 04:38:07.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-27 04:38:07.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-27 04:38:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:07.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:07.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:07.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:07.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:07.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:07.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:07.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:38:07.114][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:38:07.116][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-27 04:38:07.118][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:38:07.130][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-27 04:38:07.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:07.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:07.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:07.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:07.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:07.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:07.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:38:07.158][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-27 04:38:07.250][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:38:07.257][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-27 04:38:07.260][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:38:07.261][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:38:07.263][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:38:07.265][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:38:07.267][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:38:07.268][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:38:07.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:07.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:07.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:07.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:07.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:07.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:07.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:38:07.291][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-27 04:38:07.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:38:07.319][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:38:07.344][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-27 04:38:08.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-27 04:38:09.153][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:38:10.022][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-27 04:38:42.797][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-27 04:38:42.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-27 04:38:42.831][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:38:42.834][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:38:42.837][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:38:42.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:42.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:42.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:42.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:42.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:42.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:43.001][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[2025-03-27 04:38:43.018][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.020][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.032][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:38:43.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:38:43.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.039][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:38:43.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:38:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.046][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:38:43.048][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:38:43.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:38:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:38:43.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:43.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:43.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:38:43.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:38:43.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.073][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:43.075][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:43.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:38:43.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:38:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.093][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:38:43.095][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:38:43.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.100][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:38:43.102][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.107][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:38:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.113][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:43.115][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:43.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:43.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:38:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.127][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:43.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:43.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:38:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:38:43.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.141][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:38:43.143][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:38:43.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.148][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:38:43.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:38:43.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.155][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:38:43.156][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:38:43.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.161][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:38:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:38:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:38:43.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:38:43.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:38:43.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:43.230][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-27 04:38:43.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:43.267][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:38:43.275][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:38:43.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-27 04:38:43.279][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:38:43.282][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-27 04:38:43.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:43.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:43.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:43.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:43.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:43.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:43.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:38:43.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:38:43.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:38:43.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:38:43.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:38:43.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:43.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:43.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:43.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:43.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:43.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:43.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:38:43.378][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-27 04:38:43.379][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:38:43.382][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-27 04:38:43.384][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:38:43.386][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:38:43.387][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:38:43.389][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:38:43.390][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:38:43.392][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:38:43.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:38:43.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:38:43.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:38:43.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:38:43.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:38:43.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:38:43.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:38:43.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-27 04:38:43.431][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:38:43.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:38:43.435][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-27 04:38:44.170][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-27 04:38:45.228][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:38:45.263][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-27 04:38:45.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-27 04:39:24.861][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-27 04:39:24.886][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:39:24.901][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:39:24.905][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:39:24.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:24.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:24.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:24.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:24.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:24.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:24.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:39:24.994][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:24.996][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:24.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.001][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.022][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:39:25.028][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:39:25.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:39:25.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:39:25.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.070][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:39:25.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:39:25.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:39:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:39:25.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:39:25.137][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:39:25.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:39:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:39:25.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.170][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:39:25.172][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:39:25.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:39:25.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:39:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.201][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:39:25.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:39:25.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.216][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:39:25.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:39:25.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.244][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:25.250][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:25.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:25.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:25.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.276][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:39:25.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:39:25.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:39:25.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:39:25.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.313][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:39:25.315][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:39:25.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.329][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:39:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:39:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.396][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:39:25.402][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:39:25.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.410][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:39:25.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:39:25.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:25.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:25.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:25.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:39:25.572][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-27 04:39:25.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:39:25.682][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:39:25.698][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:39:25.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:39:25.707][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:39:25.737][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-27 04:39:25.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:25.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:25.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:25.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:25.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:25.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:25.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:39:25.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:25.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:25.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:25.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:39:25.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:25.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:25.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:25.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:25.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:25.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:25.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:39:25.850][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-27 04:39:25.851][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:39:25.858][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-27 04:39:25.860][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:39:25.866][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:39:25.868][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:39:25.873][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:39:25.875][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:39:25.881][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:39:25.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:25.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:25.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:25.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:25.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:25.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:25.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:39:25.921][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-27 04:39:25.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:39:25.931][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:39:25.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-27 04:39:40.625][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747 does not exist.
biodb.TRACE[2025-03-27 04:39:40.656][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-27 04:39:40.658][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-27 04:39:40.666][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-27 04:39:41.658][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:39:41.671][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-27 04:39:41.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-27 04:39:41.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-27 04:39:41.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:39:41.741][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:39:41.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:39:41.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:41.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:41.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:41.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:41.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:41.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:41.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:39:41.810][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:41.851][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:41.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:41.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:41.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.880][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:39:41.883][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:39:41.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.891][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.897][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:39:41.899][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:39:41.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.913][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:39:41.915][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:39:41.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.929][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:39:41.931][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:39:41.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:39:41.947][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:39:41.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.955][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.961][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:39:41.963][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:41.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:41.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:39:41.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:41.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:41.992][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:39:41.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:39:41.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:39:42.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:39:42.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.019][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:39:42.026][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:39:42.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.035][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:39:42.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:39:42.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.051][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:39:42.057][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:39:42.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:39:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:39:42.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:39:42.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:39:42.175][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-27 04:39:42.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:39:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:39:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:39:42.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:39:42.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:42.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:42.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:42.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:42.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:42.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:42.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:39:42.229][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-27 04:39:42.230][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:39:42.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-27 04:39:42.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:39:42.237][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:39:42.239][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:39:42.241][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:39:42.243][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:39:42.244][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:39:42.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:39:42.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:39:42.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:39:42.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:39:42.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:39:42.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:39:42.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:39:42.286][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-27 04:39:42.295][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:39:42.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:39:42.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-27 04:42:38.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-27 04:42:40.827][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:42:40.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-27 04:42:40.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-27 04:42:40.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-27 04:42:40.946][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:42:40.948][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:42:40.955][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:42:40.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:40.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:40.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:41.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:41.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:41.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:41.038][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.TRACE[2025-03-27 04:42:41.042][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.044][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.047][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.056][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:42:41.057][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:42:41.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.068][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:42:41.070][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:42:41.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:42:41.078][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:42:41.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.081][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.083][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:42:41.084][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:42:41.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:42:41.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:42:41.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.096][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:42:41.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.103][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:42:41.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:42:41.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.110][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:42:41.112][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:42:41.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.115][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:42:41.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:42:41.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:42:41.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:42:41.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:42:41.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:42:41.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.138][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:42:41.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:42:41.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:41.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:41.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:41.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:42:41.213][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-27 04:42:41.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:41.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:42:41.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:41.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:41.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:41.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:41.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:41.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:41.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:42:41.266][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-27 04:42:41.267][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:42:41.270][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-27 04:42:41.272][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:42:41.274][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:42:41.275][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:42:41.277][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:42:41.279][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:42:41.280][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:42:41.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:41.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:41.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:41.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:41.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:41.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:41.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:42:41.301][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-27 04:42:41.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:42:41.308][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:42:41.310][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-27 04:42:42.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-27 04:42:45.116][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:42:45.600][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-27 04:42:45.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-27 04:42:45.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-27 04:42:45.723][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:42:45.725][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:42:45.727][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:42:45.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:45.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:45.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:45.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:45.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:45.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:45.920][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.TRACE[2025-03-27 04:42:45.965][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:45.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:45.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:45.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:45.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:45.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:45.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:45.983][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:42:45.985][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:42:45.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:45.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:45.990][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:42:45.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:42:45.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:45.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:45.997][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:42:45.999][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:42:46.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.004][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:42:46.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:42:46.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.011][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:42:46.013][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:42:46.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.018][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:42:46.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:42:46.026][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:42:46.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.031][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:42:46.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:42:46.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:42:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:42:46.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.045][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:42:46.046][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:42:46.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:42:46.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:42:46.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.057][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:42:46.059][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:42:46.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:42:46.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:42:46.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:42:46.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:42:46.131][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-27 04:42:46.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:42:46.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:42:46.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:42:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:42:46.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:46.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:46.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:46.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:46.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:46.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:46.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:42:46.188][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-27 04:42:46.190][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:42:46.194][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-27 04:42:46.201][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:42:46.203][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:42:46.205][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:42:46.208][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:42:46.210][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:42:46.212][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:42:46.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:42:46.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:42:46.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:42:46.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:42:46.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:42:46.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:42:46.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:42:46.239][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-27 04:42:46.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:42:46.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:42:46.264][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-27 04:42:48.195][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.INFO [2025-03-27 04:43:36.569][private$doSendRequestLoop] Error while retrieving HTTP header: simpleWarning in max(i): no non-missing arguments to max; returning -Inf
. When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441". Retrying connection to server...
biodb.DEBUG[2025-03-27 04:43:36.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:43:36.597][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:43:36.600][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-27 04:43:40.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-27 04:43:42.437][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:43:42.455][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-27 04:43:42.470][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-27 04:43:42.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-27 04:43:42.479][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:43:42.481][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:43:42.484][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:43:42.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:43:42.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:43:42.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:43:42.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:43:42.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:43:42.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:43:42.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:43:42.541][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.545][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.556][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:43:42.558][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:43:42.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:43:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:43:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.569][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:43:42.570][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:43:42.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:43:42.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:43:42.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.582][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:43:42.583][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:43:42.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:43:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:43:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.595][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:43:42.596][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:43:42.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:43:42.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:43:42.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.607][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:43:42.609][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:43:42.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.618][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:43:42.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:43:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.625][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:43:42.627][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.630][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.632][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:43:42.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.639][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:43:42.641][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:43:42.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:43:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:43:42.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.652][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:43:42.654][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:43:42.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:43:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:43:42.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.666][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:43:42.668][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:43:42.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:43:42.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:43:42.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:43:42.698][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:43:42.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:43:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:43:42.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:43:42.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:43:42.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:43:42.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:43:42.769][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-27 04:43:42.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:43:42.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:43:42.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:43:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:43:42.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:43:42.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:43:42.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:43:55.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:43:55.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:43:55.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:43:55.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:43:55.900][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-27 04:43:55.902][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:43:58.800][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-27 04:43:58.815][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:43:58.817][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:43:58.819][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:43:58.821][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:43:58.822][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:43:58.824][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:43:58.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:43:58.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:43:58.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:43:58.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:43:58.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:43:58.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:43:58.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:43:58.852][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-27 04:43:58.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:43:58.861][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:43:58.864][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-27 04:43:59.617][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-27 04:44:13.117][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:44:13.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-27 04:44:13.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-27 04:44:13.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-27 04:44:13.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:44:13.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:44:13.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:44:13.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:13.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:13.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:13.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:13.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:13.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:13.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:44:13.195][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.197][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.208][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:13.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:13.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.214][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:13.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:13.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.221][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:13.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:13.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:13.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:13.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.236][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:13.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:13.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:13.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:13.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.248][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:13.250][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:13.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.252][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:13.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.260][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:13.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:13.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:13.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.273][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:13.275][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.279][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:13.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:13.287][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:13.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:13.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:13.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.297][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:13.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:13.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:13.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.310][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:13.311][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:13.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.314][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.316][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:13.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:13.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:13.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:13.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:13.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:13.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:13.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:13.414][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-27 04:44:13.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:13.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:13.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:13.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:13.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:13.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:13.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:13.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:13.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:13.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:13.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:13.448][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-27 04:44:13.449][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:44:13.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-27 04:44:13.453][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:44:13.454][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:44:13.456][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:44:13.457][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:44:13.459][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:44:13.460][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:44:13.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:13.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:13.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:13.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:13.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:13.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:13.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:13.478][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-27 04:44:13.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:44:13.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:44:13.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-27 04:44:14.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-27 04:44:15.832][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:44:15.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-27 04:44:15.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-27 04:44:15.875][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-27 04:44:15.877][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:44:15.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:44:15.886][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:44:15.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:15.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:15.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:15.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:17.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:17.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:17.825][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.TRACE[2025-03-27 04:44:17.889][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:17.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:17.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:17.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:17.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:17.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:17.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:17.936][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:17.938][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:17.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:17.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:17.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:17.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:17.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:17.975][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:17.985][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:17.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:17.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:18.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:18.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.021][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:18.023][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:18.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.034][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.059][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:18.065][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:18.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:18.103][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:18.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.116][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:18.126][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:18.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.137][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.162][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:18.164][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:18.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:18.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.200][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:18.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:18.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.258][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:18.259][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:18.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.293][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:18.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.304][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:18.310][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:18.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.317][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.319][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:19.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:19.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:19.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:19.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:19.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:19.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:19.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:19.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:20.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:20.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:20.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:20.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:20.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:20.037][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-27 04:44:20.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:20.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:20.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:20.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:20.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:20.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:20.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:20.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:20.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:20.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:20.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:20.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:20.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:20.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:20.206][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-27 04:44:20.216][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:44:20.230][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-27 04:44:20.283][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:44:20.285][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:44:20.287][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:44:20.293][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:44:20.295][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:44:20.302][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:44:20.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:20.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:20.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:20.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:20.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:20.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:20.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:20.355][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-27 04:44:20.372][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:44:20.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:44:20.376][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-27 04:44:39.841][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-27 04:44:46.096][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:44:46.219][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-27 04:44:46.272][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-27 04:44:46.282][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-27 04:44:46.288][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:44:46.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:44:46.297][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:44:46.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:46.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:46.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:46.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:46.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:46.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:46.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:44:46.460][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:46.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:46.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:46.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.495][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:46.501][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:46.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:44:46.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:44:46.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.534][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:46.541][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:46.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:44:46.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:44:46.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.573][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:46.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:46.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:44:46.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:44:46.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.605][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:46.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:46.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:44:46.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:44:46.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.638][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:46.639][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:44:46.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.644][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:46.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:46.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.651][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:44:46.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:46.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.658][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:46.659][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:46.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.663][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:44:46.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.762][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:46.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:46.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:44:46.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:44:46.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.797][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:46.799][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:46.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.806][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:44:46.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:44:46.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:46.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:46.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:44:46.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:44:46.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:46.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:46.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:44:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:46.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:49.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:49.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:44:49.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:44:49.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:49.880][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-27 04:44:49.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:44:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:44:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:44:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:44:49.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:49.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:49.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:50.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:50.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:50.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:50.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:50.845][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-27 04:44:50.846][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:44:50.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-27 04:44:53.814][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:44:53.853][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:44:53.855][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:44:53.857][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:44:53.859][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:44:53.860][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:44:53.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:44:53.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:44:53.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:44:53.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:44:55.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:44:55.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:44:55.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:44:55.850][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-27 04:44:59.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:44:59.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:44:59.852][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-27 04:45:34.467][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-27 04:45:43.879][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:45:50.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-27 04:46:03.815][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-27 04:46:03.884][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-27 04:46:03.892][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:46:03.894][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:46:03.898][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:46:03.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:46:03.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:46:03.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:46:03.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:46:03.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:46:03.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:46:03.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:46:04.050][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:04.052][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:04.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:04.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:04.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.072][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:46:04.078][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:46:04.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:46:04.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:46:04.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.102][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:46:04.104][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:46:04.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:46:04.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:46:04.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.133][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:46:04.135][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:46:04.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.153][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:04.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:46:04.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:46:04.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:04.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.049][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:46:08.057][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:46:08.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:46:08.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:46:08.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.158][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:46:08.160][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:46:08.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.197][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:46:08.199][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.219][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:46:08.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.236][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:46:08.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:46:08.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:46:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:46:08.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.273][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:46:08.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:46:08.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:46:08.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:46:08.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.306][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:46:08.308][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:46:08.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.322][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:46:08.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:46:08.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:46:08.344][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:46:08.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:46:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:46:08.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:46:08.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:46:08.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:46:08.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:46:08.531][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-27 04:46:08.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:46:08.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:46:08.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:46:08.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:46:08.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:46:08.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:46:08.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:46:17.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:46:17.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:46:17.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:46:17.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:46:17.850][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-27 04:46:17.856][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:46:17.946][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-27 04:46:18.026][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:46:24.946][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:46:24.991][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:46:25.049][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:46:25.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:46:25.063][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:46:25.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:46:25.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:46:25.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:46:25.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:46:25.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:46:25.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:46:25.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:46:25.192][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-27 04:46:25.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:46:25.289][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:46:25.292][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-27 04:48:17.840][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861 does not exist.
biodb.TRACE[2025-03-27 04:48:17.851][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-27 04:48:17.854][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-27 04:48:17.856][getBaseUrlRequestResult] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-27 04:48:23.245][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:23.358][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-27 04:48:23.381][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-27 04:48:23.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-27 04:48:23.406][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:23.408][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:23.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:23.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:23.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:23.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:23.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:23.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:23.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:23.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:23.452][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.454][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.598][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:23.600][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:23.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.604][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:23.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:23.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.611][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:23.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:23.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:23.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:23.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.623][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:23.625][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:23.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:23.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:23.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:23.637][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:23.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:23.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:23.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.651][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:23.652][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:23.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.657][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:23.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.663][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:23.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.669][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:23.671][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:23.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.674][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:23.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:23.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.682][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:23.683][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:23.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.686][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:23.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:23.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.697][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:23.698][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:23.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.703][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:23.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.709][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:23.711][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:23.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.715][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:23.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:23.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:23.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:23.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:23.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:23.808][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-27 04:48:23.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:23.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:23.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:23.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:23.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:23.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:23.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:23.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:23.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:23.857][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-27 04:48:23.873][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:24.831][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-27 04:48:24.854][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:24.856][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:24.857][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:24.858][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:24.860][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:24.861][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:24.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:24.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:24.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:24.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:24.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:24.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:24.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:24.888][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-27 04:48:24.926][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:24.927][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:24.929][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-27 04:48:26.174][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-27 04:48:26.951][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:26.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-27 04:48:26.959][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-27 04:48:26.963][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-27 04:48:26.965][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:26.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:26.968][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:26.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:26.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:26.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:26.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:26.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:26.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:26.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:26.987][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:26.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:26.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:26.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:26.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:26.999][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:27.000][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:27.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:27.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.010][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:27.012][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:27.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:27.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:27.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.024][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:27.026][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:27.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:27.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:27.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.037][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:27.038][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:27.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:27.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:27.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.048][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:27.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:27.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.054][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:27.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.060][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:27.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.066][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:27.068][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:27.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:27.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.078][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:27.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:27.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:27.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:27.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.090][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:27.092][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:27.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.096][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:27.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:27.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.102][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:27.104][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:27.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.108][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:27.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:27.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:27.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:27.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:27.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:27.181][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-27 04:48:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:27.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:27.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:27.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:27.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:27.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:27.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:27.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:27.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:27.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:27.214][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-27 04:48:27.215][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:27.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-27 04:48:27.219][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:27.229][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:27.231][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:27.233][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:27.235][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:27.236][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:27.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:27.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:27.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:27.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:27.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:27.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:27.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:27.255][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-27 04:48:27.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:27.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:27.263][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-27 04:48:27.987][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-27 04:48:28.929][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:28.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-27 04:48:28.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-27 04:48:28.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-27 04:48:28.954][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:28.955][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:28.957][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:28.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:28.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:28.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:28.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:28.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:28.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:28.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:28.978][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:28.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:28.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:28.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:28.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:28.990][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:28.992][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:28.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:28.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:28.997][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:28.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:28.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.003][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:29.004][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:29.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:29.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:29.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.017][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:29.019][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:29.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.023][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:29.025][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:29.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.029][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:29.031][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:29.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.034][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.036][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:29.038][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.049][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:29.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:29.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:29.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:29.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.061][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:29.062][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:29.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:29.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:29.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.073][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:29.075][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:29.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:29.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.086][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:29.087][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:29.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:29.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:29.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:29.151][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-27 04:48:29.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:29.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:29.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:29.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:29.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:29.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:29.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:29.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:29.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:29.204][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-27 04:48:29.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:29.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-27 04:48:29.210][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:29.212][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:29.213][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:29.215][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:29.216][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:29.218][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:29.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:29.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:29.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:29.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:29.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:29.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:29.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:29.239][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-27 04:48:29.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:29.244][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:29.246][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-27 04:48:29.970][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-27 04:48:30.707][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:30.709][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-27 04:48:30.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-27 04:48:30.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-27 04:48:30.719][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:30.721][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:30.722][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:30.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:30.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:30.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:30.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:30.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:30.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:30.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:30.740][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.742][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.752][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:30.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:30.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:30.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.763][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:30.765][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:30.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:30.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:30.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.775][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:30.776][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:30.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:30.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:30.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:30.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:30.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.792][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:30.793][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:30.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:30.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:30.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:30.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.815][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:30.816][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:30.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:30.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.826][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:30.828][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:30.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:30.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:30.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:30.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:30.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:30.898][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-27 04:48:30.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:30.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:30.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:30.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:30.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:30.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:30.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:30.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:30.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:30.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:30.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:30.944][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-27 04:48:30.945][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:30.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-27 04:48:30.949][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:30.951][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:30.952][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:30.954][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:30.955][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:30.956][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:30.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:30.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:30.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:30.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:30.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:30.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:30.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:30.975][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-27 04:48:30.978][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:30.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:30.982][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-27 04:48:31.706][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-27 04:48:32.435][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:32.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-27 04:48:32.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-27 04:48:32.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-27 04:48:32.448][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:32.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:32.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:32.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:32.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:32.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:32.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:32.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:32.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:32.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:32.470][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.472][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.482][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:32.484][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:32.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.486][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.488][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:32.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:32.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:32.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:32.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:32.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.507][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:32.508][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:32.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:32.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:32.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.518][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:32.520][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:32.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:32.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:32.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.530][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:32.531][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:32.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.535][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:32.537][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:32.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.547][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:32.548][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:32.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:32.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:32.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.558][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:32.560][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:32.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:32.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:32.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.570][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:32.571][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:32.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:32.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:32.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:32.582][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:32.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.587][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:32.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:32.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:32.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:32.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:32.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:32.662][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-27 04:48:32.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:32.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:32.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:32.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:32.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:32.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:32.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:32.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:32.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:32.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:32.695][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-27 04:48:32.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:32.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-27 04:48:32.700][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:32.702][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:32.703][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:32.705][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:32.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:32.707][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:32.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:32.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:32.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:32.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:32.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:32.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:32.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:32.726][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-27 04:48:32.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:32.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:32.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-27 04:48:33.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-27 04:48:34.197][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:34.200][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-27 04:48:34.205][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-27 04:48:34.209][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-27 04:48:34.211][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:34.212][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:34.214][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:34.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:34.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:34.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:34.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:34.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:34.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:34.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:34.233][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.234][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.244][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:34.246][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:34.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.260][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:34.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:34.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.266][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:34.268][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:34.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:34.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:34.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:34.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:34.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:34.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:34.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.291][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:34.293][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:34.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.296][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:34.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:34.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.304][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:34.306][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:34.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.308][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.310][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:34.312][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.317][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:34.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.323][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:34.324][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:34.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:34.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:34.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.335][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:34.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:34.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:34.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:34.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.348][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:34.349][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:34.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.354][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:34.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.383][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:34.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:34.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.388][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.390][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:34.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:34.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:34.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:34.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:34.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:34.454][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-27 04:48:34.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:34.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:34.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:34.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:34.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:34.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:34.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:34.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:34.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:34.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:34.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:34.488][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-27 04:48:34.489][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:34.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-27 04:48:34.494][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:34.495][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:34.497][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:34.498][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:34.500][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:34.501][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:34.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:34.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:34.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:34.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:34.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:34.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:34.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:34.520][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-27 04:48:34.524][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:34.526][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:34.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-27 04:48:35.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-27 04:48:36.001][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:36.005][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-27 04:48:36.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-27 04:48:36.016][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-27 04:48:36.018][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:36.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:36.022][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:36.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:36.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:36.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:36.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:36.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:36.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:36.038][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.TRACE[2025-03-27 04:48:36.042][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.054][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:36.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:36.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.060][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:36.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:36.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.066][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:36.068][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:36.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.073][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:36.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:36.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.079][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:36.080][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:36.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:36.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.091][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:36.093][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:36.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.104][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:36.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:36.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.111][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:36.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:36.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:36.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:36.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.153][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:36.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:36.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:36.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:36.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.166][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:36.168][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:36.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.179][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:36.180][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:36.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.185][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:36.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:36.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:36.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:36.254][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-27 04:48:36.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:36.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:36.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:36.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:36.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:36.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:36.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:36.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:36.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:36.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:36.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:36.289][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-27 04:48:36.291][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:36.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-27 04:48:36.295][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:36.296][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:36.298][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:36.299][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:36.301][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:36.302][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:36.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:36.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:36.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:36.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:36.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:36.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:36.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:36.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-27 04:48:36.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:36.327][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:36.329][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-27 04:48:37.417][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-27 04:48:38.147][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:38.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-27 04:48:38.155][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-27 04:48:38.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-27 04:48:38.161][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:38.163][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:38.164][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:38.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:38.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:38.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:38.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:38.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:38.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:38.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:38.184][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.186][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.196][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:38.198][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:38.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.203][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:38.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:38.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.209][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:38.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:38.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.213][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:38.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:38.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.235][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:38.236][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:38.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.239][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:38.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:38.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.247][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:38.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:38.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:38.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:38.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:38.260][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:38.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.265][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:38.266][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.269][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.271][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:38.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.276][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:38.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:38.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:38.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:38.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.288][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:38.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:38.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.292][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:38.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:38.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.300][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:38.301][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:38.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:38.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.311][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:38.313][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:38.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:38.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:38.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:38.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:38.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:38.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:38.378][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-27 04:48:38.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:38.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:38.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:38.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:38.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:38.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:38.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:38.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:38.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:38.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:38.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:38.411][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-27 04:48:38.413][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:38.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-27 04:48:38.417][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:38.418][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:38.420][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:38.421][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:38.423][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:38.424][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:38.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:38.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:38.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:38.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:38.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:38.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:38.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:38.443][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-27 04:48:38.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:38.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:38.450][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-27 04:48:39.183][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-27 04:48:39.925][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:39.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-27 04:48:39.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-27 04:48:39.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-27 04:48:39.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:39.939][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:39.941][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:39.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:39.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:39.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:39.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:39.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:39.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:39.991][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.TRACE[2025-03-27 04:48:39.996][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:39.998][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:39.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.001][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.009][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:40.011][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:40.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.022][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:40.024][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:40.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.035][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:40.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:40.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:40.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:40.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.048][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:40.049][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:40.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:40.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:40.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.060][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:40.062][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:40.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.066][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:40.068][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.073][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:40.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:40.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:40.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:40.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:40.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.092][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:40.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:40.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:40.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:40.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.105][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:40.106][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:40.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:40.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:40.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.118][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:40.119][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:40.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:40.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:40.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:40.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:40.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:40.195][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-27 04:48:40.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:40.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:40.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:40.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:40.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:40.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:40.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:40.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:40.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:40.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:40.229][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-27 04:48:40.231][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:40.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.INFO [2025-03-27 04:48:40.235][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-27 04:48:40.237][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:40.238][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:40.240][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:40.241][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:40.243][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:40.244][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:40.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:40.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:40.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:40.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:40.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:40.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:40.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:40.271][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-27 04:48:40.275][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:40.277][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:40.279][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-27 04:48:41.005][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-27 04:48:41.736][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:41.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-27 04:48:41.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-27 04:48:41.748][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-27 04:48:41.750][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:41.752][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:41.754][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:41.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:41.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:41.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:41.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:41.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:41.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:41.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:41.774][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.787][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:41.789][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:41.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.794][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:41.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.800][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:41.801][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:41.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.804][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:41.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.813][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:41.814][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:41.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:41.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:41.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:41.827][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:41.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.829][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:41.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:41.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.837][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:41.839][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:41.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.843][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:41.845][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.850][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:41.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.857][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:41.858][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:41.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:41.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:41.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.870][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:41.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:41.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:41.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:41.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.883][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:41.885][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:41.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:41.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:41.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.895][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:41.896][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:41.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.899][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.901][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:41.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:41.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:41.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:41.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:41.962][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-27 04:48:41.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:41.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:41.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:41.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:41.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:41.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:42.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:42.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:42.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:42.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:42.008][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-27 04:48:42.009][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:42.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-27 04:48:42.013][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:42.015][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:42.016][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:42.018][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:42.019][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:42.020][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:42.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:42.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:42.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:42.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:42.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:42.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:42.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:42.039][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-27 04:48:42.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:42.044][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:42.046][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-27 04:48:42.772][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-27 04:48:43.502][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-27 04:48:43.505][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-27 04:48:43.507][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-27 04:48:43.512][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-27 04:48:43.516][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-27 04:48:43.518][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:43.519][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:43.521][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:43.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:43.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:43.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:43.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:43.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:43.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:43.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:43.540][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.541][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.552][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:43.553][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:43.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.558][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:43.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.564][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:43.565][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:43.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:43.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:43.577][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:43.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:43.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.587][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:43.589][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:43.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.592][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.599][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:43.601][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:43.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.605][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:43.607][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.611][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:43.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:43.618][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:43.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.621][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:43.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:43.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.628][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:43.630][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:43.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:43.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:43.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:43.642][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:43.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.646][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:43.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:43.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.652][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:43.654][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:43.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.656][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:43.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:43.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:43.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:43.734][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-27 04:48:43.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:43.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:43.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:43.783][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:43.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:43.787][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:44.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:45.387][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:45.390][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-27 04:48:45.402][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-27 04:48:45.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.878][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.TRACE[2025-03-27 04:48:45.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:45.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:45.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:45.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:45.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:45.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:45.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:45.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:45.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:45.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:45.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:45.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:46.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:46.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:46.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:46.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:46.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:46.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:46.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:46.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:46.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:46.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:46.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:46.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:46.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:46.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:46.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:46.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:46.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:46.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:46.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:46.069][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[2025-03-27 04:48:46.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:46.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:46.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:46.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:46.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:46.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:46.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:46.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:46.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:46.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:46.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:46.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:46.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:46.219][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:46.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:46.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:46.227][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:46.963][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:47.687][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:47.689][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-27 04:48:47.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-27 04:48:47.699][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:47.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:47.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:47.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:48.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:49.177][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:49.180][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-27 04:48:49.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-27 04:48:49.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:49.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:49.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:49.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:49.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:49.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:49.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:49.205][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-27 04:48:49.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:49.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-27 04:48:49.210][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:49.211][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:49.213][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:49.214][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:49.216][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:49.217][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:49.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:49.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:49.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:49.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:49.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:49.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:49.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:49.235][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-27 04:48:49.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:49.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:49.243][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-27 04:48:49.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-27 04:48:50.718][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:50.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-27 04:48:50.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-27 04:48:50.740][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-27 04:48:50.744][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:50.747][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:50.749][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:50.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:50.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:50.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:50.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:50.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:50.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:50.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:50.775][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.777][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.789][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:50.791][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:50.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.829][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:50.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:50.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.836][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:50.838][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:50.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:50.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.850][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:50.851][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:50.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:50.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:50.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.864][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:50.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:50.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:50.879][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:50.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:50.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:50.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.891][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:50.893][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:50.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.897][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.904][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:50.905][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:50.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.908][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:50.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:50.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.916][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:50.918][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:50.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.921][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:50.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.929][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:50.930][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:50.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:50.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.941][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:50.943][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:50.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:50.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:50.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:50.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:50.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:51.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:51.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:51.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:51.014][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-27 04:48:51.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:51.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:51.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:51.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:51.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:51.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:51.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:51.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:51.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:51.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:51.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:51.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:51.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:51.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:51.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:51.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:51.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:51.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:51.078][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[2025-03-27 04:48:51.080][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-27 04:48:51.081][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:48:51.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-27 04:48:51.085][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:48:51.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:48:51.088][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:48:51.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:48:51.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:48:51.102][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:48:51.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:51.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:51.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:51.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:51.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:51.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:51.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:51.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-27 04:48:51.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:51.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:51.130][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-27 04:48:51.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-27 04:48:52.972][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:52.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-27 04:48:52.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-27 04:48:52.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-27 04:48:52.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:48:52.987][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:48:52.988][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:48:52.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:52.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:52.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:52.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.006][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.018][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:53.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:53.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.024][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:48:53.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:48:53.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.029][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:53.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:53.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:48:53.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:48:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.041][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:53.042][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:53.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:48:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:48:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.052][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:53.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:53.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:48:53.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:48:53.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.063][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:53.065][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:48:53.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.069][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:53.071][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:53.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.075][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:48:53.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:53.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.081][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.082][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.092][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:53.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:53.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:48:53.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:48:53.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.104][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:53.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:53.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.110][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:48:53.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:48:53.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.116][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:53.118][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:53.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.122][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:48:53.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:48:53.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:48:53.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:48:53.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.185][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-27 04:48:53.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.241][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:53.245][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:48:53.247][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:48:53.249][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:48:53.251][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-27 04:48:53.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.298][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.TRACE[2025-03-27 04:48:53.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.339][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.TRACE[2025-03-27 04:48:53.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.657][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.TRACE[2025-03-27 04:48:53.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.777][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.TRACE[2025-03-27 04:48:53.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.809][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[2025-03-27 04:48:53.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.872][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[2025-03-27 04:48:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:53.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:53.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:53.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:53.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:53.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:53.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:53.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:53.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:53.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:53.974][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:53.979][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:48:53.992][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-27 04:48:53.995][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:48:53.997][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-27 04:48:54.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.408][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[2025-03-27 04:48:54.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.567][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.TRACE[2025-03-27 04:48:54.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:54.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:54.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.667][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-27 04:48:54.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-27 04:48:54.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:48:54.682][biodb::testThat]
biodb.INFO [2025-03-27 04:48:54.684][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-27 04:48:54.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:48:54.687][biodb::testThat]
biodb.TRACE[2025-03-27 04:48:54.692][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-27 04:48:54.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-27 04:48:54.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:54.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:54.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:54.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:54.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:54.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:54.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:54.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:54.751][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:54.756][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:54.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:54.760][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:55.485][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:56.221][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:56.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-27 04:48:56.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-27 04:48:56.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:56.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:56.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:56.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:56.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:56.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:56.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:56.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:56.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:56.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:56.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:56.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:56.265][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:56.270][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:56.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:56.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:57.010][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:57.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:57.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-27 04:48:57.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-27 04:48:57.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:57.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:57.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:57.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:57.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:57.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:57.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:57.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:57.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:57.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:57.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:57.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:57.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:57.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:57.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:48:57.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:57.815][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:48:57.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:57.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:57.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:57.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:57.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:57.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:57.830][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[2025-03-27 04:48:57.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.844][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.845][private$selectFields]
biodb.TRACE[2025-03-27 04:48:57.847][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:48:57.848][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:48:57.849][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.851][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.857][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.862][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.863][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.865][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.872][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:48:57.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.906][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-27 04:48:57.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:57.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:57.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:57.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:57.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:57.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:57.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:57.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.955][private$selectFields]
biodb.TRACE[2025-03-27 04:48:57.956][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:48:57.958][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:48:57.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.961][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.962][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.968][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.972][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.973][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:57.975][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.976][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.980][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:48:57.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:57.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:57.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:57.999][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:48:58.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:58.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:58.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:58.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:58.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:58.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:58.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:48:58.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.027][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:58.028][private$selectFields]
biodb.TRACE[2025-03-27 04:48:58.029][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:48:58.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:48:58.032][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:58.034][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.035][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.038][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.043][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.045][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:58.046][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:48:58.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.049][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.053][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:48:58.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:48:58.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.072][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-27 04:48:58.073][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:48:58.075][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:48:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:48:58.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:48:58.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:48:58.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:48:58.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:48:58.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:48:58.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:48:58.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:48:58.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:48:58.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:48:58.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:48:58.225][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:58.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:58.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:58.234][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:48:58.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:48:59.691][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:48:59.694][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-27 04:48:59.700][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-27 04:48:59.705][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:48:59.709][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:48:59.711][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:48:59.713][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:00.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:01.160][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:01.163][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-27 04:49:01.169][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-27 04:49:01.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:01.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.307][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:49:01.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.433][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.435][private$selectFields]
biodb.TRACE[2025-03-27 04:49:01.437][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:01.438][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:01.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.442][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.443][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.449][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.457][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.461][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.465][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:01.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.488][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-27 04:49:01.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.585][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.587][private$selectFields]
biodb.TRACE[2025-03-27 04:49:01.589][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:01.590][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:01.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.594][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.601][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.627][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.629][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.635][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.674][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:49:01.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.704][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.705][private$selectFields]
biodb.TRACE[2025-03-27 04:49:01.706][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:01.708][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:01.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.717][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.718][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.722][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.724][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:01.725][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:01.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:01.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.751][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-27 04:49:01.752][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:49:01.754][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:49:01.767][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:49:01.778][biodb::testThat]
biodb.INFO [2025-03-27 04:49:01.779][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-27 04:49:01.781][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:01.783][biodb::testThat]
biodb.TRACE[2025-03-27 04:49:01.788][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-27 04:49:01.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-27 04:49:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:01.841][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:01.847][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:01.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-27 04:49:01.851][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:01.853][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-27 04:49:01.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.893][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:01.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:01.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-27 04:49:01.901][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:01.904][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-27 04:49:01.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:01.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:01.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:01.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:01.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:01.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:01.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:01.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:01.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:01.996][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:49:01.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.029][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.031][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.032][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.033][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.035][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.042][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.047][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.048][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.051][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.057][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.076][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-27 04:49:02.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.106][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.107][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.109][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.110][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.112][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.113][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.124][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.151][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:49:02.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.185][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.188][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.189][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.191][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.192][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.198][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.202][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.204][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.209][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.211][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-27 04:49:02.242][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:49:02.243][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:49:02.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:02.301][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:02.306][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:02.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-27 04:49:02.310][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:02.312][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-27 04:49:02.317][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:02.321][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:02.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-27 04:49:02.325][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:02.327][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-27 04:49:02.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.408][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[2025-03-27 04:49:02.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.427][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:49:02.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.443][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[2025-03-27 04:49:02.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.457][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.459][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.460][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.465][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.468][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.469][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.475][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.477][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.480][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.492][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.494][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.515][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-27 04:49:02.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.543][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.544][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.554][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.561][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.568][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:49:02.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.616][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.617][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.618][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.620][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.623][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.627][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.628][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.632][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.635][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.636][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.639][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.640][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.659][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-27 04:49:02.661][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:49:02.662][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:49:02.675][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:02.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:02.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:49:02.686][biodb::testThat]
biodb.INFO [2025-03-27 04:49:02.687][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-27 04:49:02.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:02.690][biodb::testThat]
biodb.TRACE[2025-03-27 04:49:02.694][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-27 04:49:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-27 04:49:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:02.756][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:02.761][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:02.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-27 04:49:02.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:02.768][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-27 04:49:02.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.808][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:02.813][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:02.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-27 04:49:02.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:02.819][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-27 04:49:02.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.869][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.TRACE[2025-03-27 04:49:02.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:02.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:02.886][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:49:02.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.914][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.915][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.916][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.917][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.919][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.920][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.922][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.925][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.927][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.931][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.932][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.939][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:02.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.956][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-27 04:49:02.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:02.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:02.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:02.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:02.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:02.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:02.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:02.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.983][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.984][private$selectFields]
biodb.TRACE[2025-03-27 04:49:02.985][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:02.986][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:02.988][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:02.989][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.993][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.994][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:02.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:02.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:02.999][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.001][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:03.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.035][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:49:03.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.049][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[2025-03-27 04:49:03.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.061][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.062][private$selectFields]
biodb.TRACE[2025-03-27 04:49:03.063][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:03.065][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:03.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.067][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.072][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.077][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.078][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.080][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.081][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.087][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:03.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.104][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-27 04:49:03.106][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:49:03.107][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:49:03.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:03.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:03.176][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:03.180][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:03.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-27 04:49:03.184][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:03.186][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-27 04:49:03.190][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:03.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:03.196][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-27 04:49:03.198][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:03.200][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-27 04:49:03.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:03.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:03.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:03.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:03.307][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-27 04:49:03.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.335][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.336][private$selectFields]
biodb.TRACE[2025-03-27 04:49:03.338][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:03.339][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:03.340][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.342][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.347][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.353][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.354][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.362][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:03.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.382][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-27 04:49:03.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.409][private$selectFields]
biodb.TRACE[2025-03-27 04:49:03.410][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:03.412][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:03.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.425][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.426][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.427][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.429][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.433][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:03.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.451][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-27 04:49:03.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:03.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.478][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.480][private$selectFields]
biodb.TRACE[2025-03-27 04:49:03.491][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-27 04:49:03.495][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-27 04:49:03.496][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.499][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.515][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-27 04:49:03.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.546][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.552][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.555][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-27 04:49:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:03.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:03.579][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-27 04:49:03.581][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-27 04:49:03.583][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-27 04:49:03.617][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:03.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-27 04:49:03.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:03.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-27 04:49:03.628][biodb::testThat]
biodb.INFO [2025-03-27 04:49:03.629][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-27 04:49:03.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:03.632][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:03.635][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-27 04:49:03.636][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:49:03.639][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-27 04:49:03.641][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:49:03.643][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:49:03.644][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:49:03.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:03.647][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:49:03.649][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:49:03.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:03.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:03.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:03.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:03.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:03.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:03.667][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.DEBUG[2025-03-27 04:49:03.668][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-27 04:49:03.673][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:03.674][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:03.676][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-27 04:49:04.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-27 04:49:05.129][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:05.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-27 04:49:05.137][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-27 04:49:05.140][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-27 04:49:05.142][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:49:05.144][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:49:05.145][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:49:05.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:05.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:05.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:05.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:05.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:05.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:05.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:05.164][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.169][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.177][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:05.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:05.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.183][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:05.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:05.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.189][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:05.191][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:05.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.195][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:05.197][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:05.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:05.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:05.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.207][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:05.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:05.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.213][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:05.215][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:05.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.217][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.219][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:05.221][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:05.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.225][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:05.227][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:05.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:05.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:05.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:05.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:05.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:05.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:05.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:05.305][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-27 04:49:05.306][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-27 04:49:05.316][biodb::testThat]
biodb.INFO [2025-03-27 04:49:05.318][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-27 04:49:05.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:05.320][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:05.334][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-27 04:49:05.336][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-27 04:49:05.337][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-27 04:49:05.339][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-27 04:49:05.341][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-27 04:49:05.342][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:49:05.344][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:49:05.345][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:05.347][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:49:05.348][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:49:05.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:05.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:05.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:05.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:05.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:05.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:05.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:05.367][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-27 04:49:05.370][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:05.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:05.374][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-27 04:49:07.506][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-27 04:49:08.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:08.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-27 04:49:08.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-27 04:49:08.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:08.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:08.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:08.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:08.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:08.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:08.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:08.254][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-27 04:49:08.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:08.260][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:08.262][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-27 04:49:10.162][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-27 04:49:10.897][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:10.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-27 04:49:10.904][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-27 04:49:10.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:10.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:10.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:10.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:10.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:10.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:10.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:10.921][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-27 04:49:10.925][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:10.926][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:10.928][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-27 04:49:11.664][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-27 04:49:12.394][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:12.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-27 04:49:12.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-27 04:49:12.407][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-27 04:49:12.409][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:49:12.412][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-27 04:49:12.414][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-27 04:49:12.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:12.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:12.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:12.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:12.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:12.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:12.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:12.435][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.447][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:12.449][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:12.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.453][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:12.455][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:12.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:12.461][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:12.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.465][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.466][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.498][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:12.499][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:12.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:12.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:12.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:12.518][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:12.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:12.524][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:12.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.526][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:12.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:12.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:12.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:12.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:12.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:12.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:12.579][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.TRACE[2025-03-27 04:49:12.582][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.593][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:12.595][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:12.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:12.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.605][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:12.606][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:12.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:12.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.616][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:12.617][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:12.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:12.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:12.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.627][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.629][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.639][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.640][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.643][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.650][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:12.652][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:12.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:12.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:12.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.663][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.666][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.673][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:12.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:12.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.677][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:12.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:12.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.685][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:12.686][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:12.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.691][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:12.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:12.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.697][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:12.698][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:12.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:12.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:12.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:12.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:12.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:12.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:12.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:12.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:12.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:12.784][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.TRACE[2025-03-27 04:49:12.790][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.792][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.803][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:12.805][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:12.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:12.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.816][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:12.818][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:12.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:12.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:12.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.828][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:12.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:12.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:12.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:12.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.841][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.843][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:12.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.854][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.855][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:12.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.866][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:12.868][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:12.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.871][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.873][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:12.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:12.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.879][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:12.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.891][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:12.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:12.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.904][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:12.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:12.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:12.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.917][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:12.919][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:12.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.922][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:12.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:12.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:12.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:12.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:12.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:12.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:12.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:13.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:13.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:13.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:13.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:13.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:13.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:13.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:13.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:13.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:13.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:13.041][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-27 04:49:13.043][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-27 04:49:13.044][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-27 04:49:13.062][biodb::testThat]
biodb.INFO [2025-03-27 04:49:13.064][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-27 04:49:13.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:13.066][biodb::testThat]
biodb.INFO [2025-03-27 04:49:13.102][biodb::testThat]
biodb.INFO [2025-03-27 04:49:13.103][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-27 04:49:13.105][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:13.106][biodb::testThat]
biodb.INFO [2025-03-27 04:49:13.118][biodb::testThat]
biodb.INFO [2025-03-27 04:49:13.119][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-27 04:49:13.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:13.122][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:13.126][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:13.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:13.132][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:13.135][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:14.503][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:16.514][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:16.517][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-27 04:49:16.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-27 04:49:16.538][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:16.539][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:16.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:16.542][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:16.543][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:16.545][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:16.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:16.547][ef$get] fields variable is a list.
biodb.INFO [2025-03-27 04:49:16.549][biodb::testThat]
biodb.INFO [2025-03-27 04:49:16.550][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-27 04:49:16.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:16.553][biodb::testThat]
biodb.ERROR[2025-03-27 04:49:16.572][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-27 04:49:16.598][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-27 04:49:16.617][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-27 04:49:16.619][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-27 04:49:16.621][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-27 04:49:16.622][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-27 04:49:16.623][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:16.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:16.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:16.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:16.628][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-27 04:49:16.645][biodb::testContext]
biodb.INFO [2025-03-27 04:49:16.646][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:16.656][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-27 04:49:16.663][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:16.665][biodb::testContext]
biodb.INFO [2025-03-27 04:49:16.668][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:16.670][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:16.675][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:16.677][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-27 04:49:16.678][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.683][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-27 04:49:16.685][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.690][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-27 04:49:16.692][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.697][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-27 04:49:16.699][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-27 04:49:16.700][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-27 04:49:16.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.705][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-27 04:49:16.707][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-27 04:49:16.708][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.713][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-27 04:49:16.715][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-27 04:49:16.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.720][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-27 04:49:16.722][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-27 04:49:16.723][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-27 04:49:16.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.727][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[2025-03-27 04:49:16.728][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-27 04:49:16.730][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.735][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-27 04:49:16.736][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-27 04:49:16.738][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-27 04:49:16.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.743][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:16.744][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-27 04:49:16.746][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-27 04:49:16.747][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-27 04:49:16.749][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-27 04:49:16.750][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-27 04:49:16.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.755][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-27 04:49:16.757][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-27 04:49:16.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.760][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.DEBUG[2025-03-27 04:49:16.762][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-27 04:49:16.763][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-27 04:49:16.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.768][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-27 04:49:16.770][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-27 04:49:16.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.775][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-27 04:49:16.777][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-27 04:49:16.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.782][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-27 04:49:16.783][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-27 04:49:16.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.787][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.DEBUG[2025-03-27 04:49:16.789][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:16.790][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-27 04:49:16.796][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-27 04:49:16.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.801][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-27 04:49:16.803][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-27 04:49:16.805][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-27 04:49:16.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:16.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.809][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.DEBUG[2025-03-27 04:49:16.810][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-27 04:49:16.813][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.815][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-27 04:49:16.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:16.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.825][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:16.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:16.828][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.829][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-27 04:49:16.831][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:16.832][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.834][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.835][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:16.835][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:16.835][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:16.835][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:16.835][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:16.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:16.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:16.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.847][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.848][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:16.849][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:16.851][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.852][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.854][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-27 04:49:16.857][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.858][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:16.860][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.861][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:16.863][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.866][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.867][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.869][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:16.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:16.872][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.873][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-27 04:49:16.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:16.876][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:16.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:16.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:16.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:16.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:16.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:16.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:16.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.889][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.891][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.892][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:16.894][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:16.895][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.897][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.898][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-27 04:49:16.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.903][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-27 04:49:16.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:16.907][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.922][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.923][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:16.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:16.926][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.928][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-27 04:49:16.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:16.931][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.934][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.935][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:16.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:16.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.945][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:16.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:16.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.951][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.953][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-27 04:49:16.955][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.957][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:16.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:16.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.964][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.967][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:16.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:16.970][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.971][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-27 04:49:16.973][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:16.974][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.976][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:16.977][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.978][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:16.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.982][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:16.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:16.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:16.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:16.988][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:16.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:16.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:16.993][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:16.995][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:16.997][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:16.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:16.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.061][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[2025-03-27 04:49:17.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.108][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-27 04:49:17.110][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-27 04:49:17.112][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-27 04:49:17.114][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-27 04:49:17.116][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:17.118][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-27 04:49:17.120][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:17.122][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:17.124][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-27 04:49:17.126][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-27 04:49:17.128][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:17.130][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-27 04:49:17.132][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:17.135][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:17.137][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-27 04:49:17.139][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-27 04:49:17.141][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-27 04:49:17.143][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-27 04:49:17.145][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:17.147][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-27 04:49:17.150][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-27 04:49:17.152][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-27 04:49:17.154][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-27 04:49:17.435][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-27 04:49:17.438][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-27 04:49:17.440][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-27 04:49:17.442][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-27 04:49:17.443][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-27 04:49:17.445][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-27 04:49:17.447][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-27 04:49:17.449][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-27 04:49:17.451][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-27 04:49:17.453][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-27 04:49:17.455][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-27 04:49:17.457][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-27 04:49:17.459][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-27 04:49:17.461][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-27 04:49:17.463][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-27 04:49:17.465][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-27 04:49:17.467][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-27 04:49:17.469][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-27 04:49:17.471][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-27 04:49:17.473][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-27 04:49:17.475][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-27 04:49:17.477][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-27 04:49:17.479][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-27 04:49:17.481][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-27 04:49:17.483][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-27 04:49:17.485][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-27 04:49:17.487][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-27 04:49:17.489][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-27 04:49:17.491][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-27 04:49:17.493][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-27 04:49:17.494][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-27 04:49:17.496][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-27 04:49:17.498][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-27 04:49:17.500][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-27 04:49:17.502][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-27 04:49:17.504][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-27 04:49:17.506][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-27 04:49:17.508][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-27 04:49:17.510][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-27 04:49:17.512][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-27 04:49:17.514][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-27 04:49:17.516][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-27 04:49:17.518][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-27 04:49:17.520][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:17.522][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:17.524][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-27 04:49:17.526][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-27 04:49:17.528][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-27 04:49:17.530][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-27 04:49:17.532][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-27 04:49:17.533][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-27 04:49:17.535][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-27 04:49:17.537][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-27 04:49:17.539][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-27 04:49:17.541][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-27 04:49:17.543][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-27 04:49:17.545][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-27 04:49:17.547][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-27 04:49:17.549][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-27 04:49:17.551][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-27 04:49:17.553][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-27 04:49:17.555][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:17.557][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:17.558][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.560][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.561][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[2025-03-27 04:49:17.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.670][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[2025-03-27 04:49:17.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:17.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:17.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:17.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:17.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:17.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:17.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:17.726][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:17.729][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-27 04:49:17.732][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:17.733][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-27 04:49:17.734][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:17.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:17.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:17.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:17.740][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:17.741][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-27 04:49:17.743][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-27 04:49:17.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:17.746][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:17.747][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-27 04:49:17.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-27 04:49:17.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-27 04:49:17.751][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:17.753][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:17.753][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:17.753][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:17.754][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-27 04:49:17.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:17.757][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:17.758][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:17.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:17.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:17.762][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:17.764][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:17.764][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-27 04:49:17.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:17.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:17.768][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:17.769][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-27 04:49:17.769][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-27 04:49:17.771][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:17.773][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:17.775][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-27 04:49:17.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:17.780][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:17.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:17.786][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-27 04:49:17.788][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-27 04:49:17.790][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-27 04:49:17.792][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-27 04:49:17.793][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:17.795][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:17.797][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-27 04:49:17.798][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-27 04:49:17.800][biodb::testThat]
biodb.INFO [2025-03-27 04:49:17.801][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-27 04:49:17.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:17.804][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:17.809][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-27 04:49:17.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:17.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:17.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-27 04:49:18.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-27 04:49:19.445][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:19.448][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-27 04:49:19.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-27 04:49:19.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:19.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:19.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:19.466][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:20.202][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:21.951][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:21.954][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-27 04:49:21.960][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-27 04:49:21.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:21.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:21.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:21.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:21.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:21.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:21.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:21.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:21.984][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:21.985][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:21.988][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:22.722][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:29.136][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:29.139][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-27 04:49:29.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-27 04:49:29.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.221][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:29.225][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:29.227][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-27 04:49:29.229][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:29.231][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-27 04:49:29.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:29.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:29.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-27 04:49:29.258][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:29.260][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-27 04:49:29.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:29.299][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:29.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-27 04:49:29.303][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:29.305][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-27 04:49:29.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.323][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:29.327][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:29.329][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-27 04:49:29.331][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:29.333][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-27 04:49:29.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:29.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:29.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:29.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:29.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:29.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:29.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:29.350][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:29.355][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:29.356][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:29.359][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:31.749][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:32.481][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:32.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-27 04:49:32.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-27 04:49:32.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:32.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:32.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:32.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:32.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:32.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:32.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-27 04:49:32.520][biodb::testThat]
biodb.INFO [2025-03-27 04:49:32.521][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-27 04:49:32.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:32.524][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:32.529][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:32.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:32.536][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:32.539][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:33.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:34.002][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:34.005][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-27 04:49:34.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-27 04:49:34.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:34.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:34.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:34.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:34.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:34.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:34.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:34.035][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:34.039][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:34.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:34.064][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:34.789][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:36.538][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:36.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-27 04:49:36.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-27 04:49:36.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:36.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:36.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:36.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-27 04:49:36.569][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-27 04:49:36.571][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-27 04:49:36.572][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-27 04:49:36.574][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-27 04:49:36.575][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:36.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:36.578][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.580][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-27 04:49:36.587][biodb::testContext]
biodb.INFO [2025-03-27 04:49:36.588][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:36.590][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-27 04:49:36.591][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:36.593][biodb::testContext]
biodb.INFO [2025-03-27 04:49:36.595][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:36.598][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:36.602][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:36.604][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-27 04:49:36.605][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.611][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-27 04:49:36.612][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.618][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-27 04:49:36.619][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.624][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-27 04:49:36.626][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-27 04:49:36.627][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-27 04:49:36.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.633][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-27 04:49:36.634][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-27 04:49:36.636][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.641][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-27 04:49:36.642][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-27 04:49:36.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.648][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-27 04:49:36.649][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-27 04:49:36.651][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-27 04:49:36.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.656][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-27 04:49:36.657][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.663][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-27 04:49:36.664][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-27 04:49:36.666][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-27 04:49:36.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.671][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:36.672][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-27 04:49:36.674][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-27 04:49:36.675][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-27 04:49:36.676][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-27 04:49:36.678][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-27 04:49:36.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.683][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-27 04:49:36.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-27 04:49:36.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.690][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-27 04:49:36.691][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-27 04:49:36.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.696][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-27 04:49:36.698][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-27 04:49:36.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.703][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-27 04:49:36.704][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-27 04:49:36.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.709][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-27 04:49:36.710][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-27 04:49:36.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.715][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:36.717][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-27 04:49:36.722][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-27 04:49:36.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.727][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-27 04:49:36.728][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-27 04:49:36.730][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-27 04:49:36.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.733][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[2025-03-27 04:49:36.735][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-27 04:49:36.737][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.739][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-27 04:49:36.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:36.743][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.744][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.747][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.748][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:36.750][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:36.751][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.752][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-27 04:49:36.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:36.755][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.758][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:36.758][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:36.758][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:36.758][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:36.758][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:36.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:36.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:36.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.768][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:36.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:36.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.773][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.775][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-27 04:49:36.778][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.779][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:36.780][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.794][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:36.795][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.798][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.801][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:36.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:36.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.805][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-27 04:49:36.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:36.807][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.809][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.810][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:36.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:36.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:36.810][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:36.810][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:36.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:36.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.815][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:36.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.820][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:36.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:36.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.825][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.826][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-27 04:49:36.829][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.830][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-27 04:49:36.831][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.833][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:36.834][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.835][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.837][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.840][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:36.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:36.842][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.844][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-27 04:49:36.845][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:36.846][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.849][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:36.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.854][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:36.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.858][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.859][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:36.861][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:36.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.864][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.866][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-27 04:49:36.868][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.869][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:36.871][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.872][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:36.873][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.875][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.879][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:36.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:36.881][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.883][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-27 04:49:36.884][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:36.885][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.887][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:36.888][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.889][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:36.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:36.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:36.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:36.897][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:36.898][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:36.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:36.902][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:36.903][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:36.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:36.907][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.920][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[2025-03-27 04:49:36.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.932][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[2025-03-27 04:49:36.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.962][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.DEBUG[2025-03-27 04:49:36.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:36.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:36.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:36.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:36.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:36.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.012][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-27 04:49:37.014][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-27 04:49:37.016][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-27 04:49:37.018][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-27 04:49:37.027][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:37.029][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-27 04:49:37.031][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:37.033][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:37.035][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-27 04:49:37.037][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-27 04:49:37.039][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:37.041][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-27 04:49:37.042][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:37.044][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:37.046][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-27 04:49:37.048][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-27 04:49:37.050][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-27 04:49:37.052][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-27 04:49:37.054][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:37.056][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-27 04:49:37.058][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-27 04:49:37.060][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-27 04:49:37.061][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-27 04:49:37.063][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-27 04:49:37.065][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-27 04:49:37.067][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-27 04:49:37.069][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-27 04:49:37.071][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-27 04:49:37.073][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-27 04:49:37.075][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-27 04:49:37.077][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-27 04:49:37.079][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-27 04:49:37.081][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-27 04:49:37.082][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-27 04:49:37.084][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-27 04:49:37.086][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-27 04:49:37.088][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-27 04:49:37.090][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-27 04:49:37.092][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-27 04:49:37.094][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-27 04:49:37.096][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-27 04:49:37.098][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-27 04:49:37.100][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-27 04:49:37.102][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-27 04:49:37.104][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-27 04:49:37.106][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-27 04:49:37.107][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-27 04:49:37.109][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-27 04:49:37.111][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-27 04:49:37.113][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-27 04:49:37.115][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-27 04:49:37.117][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-27 04:49:37.119][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-27 04:49:37.121][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-27 04:49:37.123][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-27 04:49:37.124][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-27 04:49:37.126][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-27 04:49:37.128][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-27 04:49:37.130][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-27 04:49:37.132][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-27 04:49:37.134][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-27 04:49:37.136][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-27 04:49:37.138][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-27 04:49:37.140][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-27 04:49:37.141][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-27 04:49:37.143][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-27 04:49:37.145][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:37.147][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:37.149][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-27 04:49:37.151][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-27 04:49:37.153][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-27 04:49:37.155][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-27 04:49:37.157][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-27 04:49:37.158][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-27 04:49:37.160][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-27 04:49:37.162][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-27 04:49:37.164][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-27 04:49:37.166][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-27 04:49:37.168][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-27 04:49:37.170][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-27 04:49:37.172][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-27 04:49:37.173][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-27 04:49:37.175][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-27 04:49:37.177][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-27 04:49:37.179][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:37.181][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:37.182][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.184][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.292][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[2025-03-27 04:49:37.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:37.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:37.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:37.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:37.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:37.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:37.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:37.346][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:37.348][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-27 04:49:37.351][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:37.352][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-27 04:49:37.354][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:37.355][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:37.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:37.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:37.360][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:37.361][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-27 04:49:37.362][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-27 04:49:37.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:37.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:37.367][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-27 04:49:37.368][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-27 04:49:37.370][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-27 04:49:37.371][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:37.373][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:37.373][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:37.373][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:37.374][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-27 04:49:37.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:37.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:37.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:37.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:37.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:37.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:37.383][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:37.383][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-27 04:49:37.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:37.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:37.387][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:37.395][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-27 04:49:37.395][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-27 04:49:37.398][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:37.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:37.405][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-27 04:49:37.407][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:37.409][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:37.412][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:37.418][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-27 04:49:37.419][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-27 04:49:37.421][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-27 04:49:37.423][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-27 04:49:37.425][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:37.427][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:37.429][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-27 04:49:37.430][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-27 04:49:37.433][biodb::testThat]
biodb.INFO [2025-03-27 04:49:37.434][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-27 04:49:37.436][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:37.437][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:37.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-27 04:49:37.448][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:37.450][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-27 04:49:37.452][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:37.455][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-27 04:49:37.461][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:37.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:37.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:37.470][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-27 04:49:38.195][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-27 04:49:38.929][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:38.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-27 04:49:38.938][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-27 04:49:38.949][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-27 04:49:38.951][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-27 04:49:38.953][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-27 04:49:38.954][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-27 04:49:38.955][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:38.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:38.958][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:38.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:38.961][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:38.962][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.INFO [2025-03-27 04:49:38.968][biodb::testContext]
biodb.INFO [2025-03-27 04:49:38.969][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:38.970][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-27 04:49:38.972][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-27 04:49:38.973][biodb::testContext]
biodb.INFO [2025-03-27 04:49:38.976][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:38.978][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:38.983][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:39.001][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-27 04:49:39.003][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.008][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-27 04:49:39.009][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.015][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-27 04:49:39.016][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.022][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-27 04:49:39.023][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-27 04:49:39.025][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-27 04:49:39.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.030][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-27 04:49:39.031][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-27 04:49:39.033][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.038][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-27 04:49:39.039][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-27 04:49:39.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.044][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-27 04:49:39.046][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-27 04:49:39.047][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-27 04:49:39.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.052][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-27 04:49:39.054][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.059][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-27 04:49:39.060][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-27 04:49:39.062][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-27 04:49:39.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.067][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:39.068][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-27 04:49:39.070][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-27 04:49:39.071][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-27 04:49:39.073][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-27 04:49:39.074][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-27 04:49:39.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.078][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[2025-03-27 04:49:39.079][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-27 04:49:39.081][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-27 04:49:39.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.086][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-27 04:49:39.087][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-27 04:49:39.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.092][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-27 04:49:39.094][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-27 04:49:39.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.099][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-27 04:49:39.101][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-27 04:49:39.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.106][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-27 04:49:39.107][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-27 04:49:39.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.112][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-27 04:49:39.114][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-27 04:49:39.118][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-27 04:49:39.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.124][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-27 04:49:39.125][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-27 04:49:39.127][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-27 04:49:39.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.132][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-27 04:49:39.135][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.136][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-27 04:49:39.137][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:39.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.143][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.144][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.146][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:39.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:39.148][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.150][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-27 04:49:39.151][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:39.152][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.155][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:39.155][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:39.155][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:39.155][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:39.155][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:39.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:39.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:39.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.166][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.167][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:39.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:39.170][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.171][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.173][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-27 04:49:39.175][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.176][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:39.178][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.179][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:39.181][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:39.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:39.189][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.190][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-27 04:49:39.192][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:39.193][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.194][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.196][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:39.196][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:39.196][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:39.196][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-27 04:49:39.196][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-27 04:49:39.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:39.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.200][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.201][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:39.203][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.205][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.207][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:39.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:39.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.212][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.213][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-27 04:49:39.216][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.217][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-27 04:49:39.219][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:39.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.223][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.224][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.226][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.227][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-27 04:49:39.228][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:39.230][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.231][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-27 04:49:39.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:39.234][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.237][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:39.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.249][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:39.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.253][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.254][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:39.257][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:39.258][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.259][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.261][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-27 04:49:39.264][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.265][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-27 04:49:39.266][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:39.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.272][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.273][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.274][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-27 04:49:39.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:39.277][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.278][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-27 04:49:39.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:39.281][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.284][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.285][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-27 04:49:39.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.289][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:39.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.294][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:39.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:39.298][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.299][self$setPropertyValue]
biodb.DEBUG[2025-03-27 04:49:39.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:39.302][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.407][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-27 04:49:39.409][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-27 04:49:39.411][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-27 04:49:39.413][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-27 04:49:39.415][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:39.417][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-27 04:49:39.419][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:39.421][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:39.423][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-27 04:49:39.425][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-27 04:49:39.426][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:39.428][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-27 04:49:39.430][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-27 04:49:39.432][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-27 04:49:39.434][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-27 04:49:39.436][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-27 04:49:39.438][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-27 04:49:39.440][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-27 04:49:39.442][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:39.444][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-27 04:49:39.446][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-27 04:49:39.448][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-27 04:49:39.450][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-27 04:49:39.452][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-27 04:49:39.453][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-27 04:49:39.455][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-27 04:49:39.457][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-27 04:49:39.459][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-27 04:49:39.461][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-27 04:49:39.463][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-27 04:49:39.465][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-27 04:49:39.474][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-27 04:49:39.476][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-27 04:49:39.478][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-27 04:49:39.480][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-27 04:49:39.482][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-27 04:49:39.484][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-27 04:49:39.486][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-27 04:49:39.488][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-27 04:49:39.490][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-27 04:49:39.492][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-27 04:49:39.494][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-27 04:49:39.496][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-27 04:49:39.497][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-27 04:49:39.499][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-27 04:49:39.501][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-27 04:49:39.503][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-27 04:49:39.505][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-27 04:49:39.507][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-27 04:49:39.509][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-27 04:49:39.511][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-27 04:49:39.513][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-27 04:49:39.515][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-27 04:49:39.517][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-27 04:49:39.519][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-27 04:49:39.521][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-27 04:49:39.523][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-27 04:49:39.524][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-27 04:49:39.526][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-27 04:49:39.528][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-27 04:49:39.530][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-27 04:49:39.532][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-27 04:49:39.534][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-27 04:49:39.536][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-27 04:49:39.538][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-27 04:49:39.540][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-27 04:49:39.542][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:39.543][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:39.545][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-27 04:49:39.547][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-27 04:49:39.549][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-27 04:49:39.551][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-27 04:49:39.553][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-27 04:49:39.555][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-27 04:49:39.557][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-27 04:49:39.559][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-27 04:49:39.561][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-27 04:49:39.562][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-27 04:49:39.564][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-27 04:49:39.566][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-27 04:49:39.568][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-27 04:49:39.570][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-27 04:49:39.572][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-27 04:49:39.574][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-27 04:49:39.576][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-27 04:49:39.577][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-27 04:49:39.579][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.581][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.691][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[2025-03-27 04:49:39.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-27 04:49:39.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.733][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[2025-03-27 04:49:39.735][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-devel_2025-02-19/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-27 04:49:39.737][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-27 04:49:39.740][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.741][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.742][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.744][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-27 04:49:39.745][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.748][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.749][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-27 04:49:39.751][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-27 04:49:39.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-27 04:49:39.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.755][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-27 04:49:39.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-27 04:49:39.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-27 04:49:39.759][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-27 04:49:39.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-27 04:49:39.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-27 04:49:39.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-27 04:49:39.762][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-27 04:49:39.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.764][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-27 04:49:39.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-27 04:49:39.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-27 04:49:39.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-27 04:49:39.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:39.771][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-27 04:49:39.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-27 04:49:39.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-27 04:49:39.775][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-27 04:49:39.776][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-27 04:49:39.776][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-27 04:49:39.778][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-27 04:49:39.780][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-27 04:49:39.782][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-27 04:49:39.784][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-27 04:49:39.786][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-27 04:49:39.789][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-27 04:49:39.793][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-27 04:49:39.795][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-27 04:49:39.796][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-27 04:49:39.798][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-27 04:49:39.800][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:39.801][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-27 04:49:39.803][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-27 04:49:39.804][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-27 04:49:39.806][biodb::testThat]
biodb.INFO [2025-03-27 04:49:39.807][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-27 04:49:39.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-27 04:49:39.810][biodb::testThat]
biodb.DEBUG[2025-03-27 04:49:39.814][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-27 04:49:39.819][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:39.820][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-27 04:49:39.822][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:39.824][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-27 04:49:39.828][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-27 04:49:39.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-27 04:49:39.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-27 04:49:39.836][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-27 04:49:39.837][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-27 04:49:39.843][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-27 04:49:39.845][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-27 04:49:39.847][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-27 04:49:39.849][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-27 04:49:39.850][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-27 04:49:39.852][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-27 04:49:39.853][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-27 04:49:39.855][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-27 04:49:39.856][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-27 04:49:39.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:39.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:39.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:39.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:39.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:39.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:39.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-27 04:49:39.874][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-27 04:49:39.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-27 04:49:39.879][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-27 04:49:39.880][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-27 04:49:40.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-27 04:49:41.889][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-27 04:49:41.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-27 04:49:41.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-27 04:49:41.910][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-27 04:49:41.913][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-27 04:49:41.916][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-27 04:49:41.918][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-27 04:49:41.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-27 04:49:41.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:41.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:41.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:41.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:41.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:41.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-27 04:49:41.955][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:41.957][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:41.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:41.960][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:41.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:41.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:41.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:41.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:41.971][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:41.973][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:41.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:41.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:41.980][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-27 04:49:41.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-27 04:49:42.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.038][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:42.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:42.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.044][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-27 04:49:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-27 04:49:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.054][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-27 04:49:42.056][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-27 04:49:42.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.063][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-27 04:49:42.065][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-27 04:49:42.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.071][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:42.073][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:42.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.079][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:42.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-27 04:49:42.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.086][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:42.088][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:42.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.091][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-27 04:49:42.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-27 04:49:42.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:42.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:42.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:42.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-27 04:49:42.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.116][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:42.118][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:42.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.121][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-27 04:49:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-27 04:49:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:42.135][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:42.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-27 04:49:42.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-27 04:49:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:42.151][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:42.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-27 04:49:42.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-27 04:49:42.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-27 04:49:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-27 04:49:42.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-27 04:49:42.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-27 04:49:42.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-27 04:49:42.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-27 04:49:42.243][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-27 04:49:42.250][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-27 04:49:42.253][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-27 04:49:42.255][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-27 04:49:42.257][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-27 04:49:42.259][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-27 04:49:42.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-27 04:49:42.263][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-27 04:49:42.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-27 04:49:42.266][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-27 04:49:42.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
28.113 157.898 716.229
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.284 | 0.041 | 4.169 | |
| ChebiEntry | 0.231 | 0.001 | 0.504 | |