Pierrick Roger
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: biodbChebi |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2025-03-07 05:42:52 -0000 (Fri, 07 Mar 2025) |
| EndedAt: 2025-03-07 05:51:55 -0000 (Fri, 07 Mar 2025) |
| EllapsedTime: 542.5 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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-4.4.3/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: 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 [2025-03-07 05:44:12.674][biodb::testContext]
biodb.INFO [2025-03-07 05:44:12.677][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:44:12.679][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-07 05:44:12.680][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:44:12.681][biodb::testContext]
biodb.INFO [2025-03-07 05:44:12.690][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:44:12.693][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 05:44:12.703][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:44:12.705][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 05:44:12.707][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.713][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 05:44:12.744][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.749][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 05:44:12.751][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.756][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 05:44:12.757][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 05:44:12.759][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 05:44:12.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.764][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 05:44:12.766][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 05:44:12.767][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.773][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 05:44:12.774][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 05:44:12.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.779][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 05:44:12.781][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 05:44:12.782][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 05:44:12.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.787][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 05:44:12.789][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.794][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 05:44:12.796][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 05:44:12.798][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 05:44:12.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.803][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:44:12.805][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 05:44:12.807][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 05:44:12.808][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 05:44:12.810][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 05:44:12.812][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 05:44:12.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.818][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 05:44:12.820][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 05:44:12.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.826][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 05:44:12.827][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 05:44:12.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.833][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 05:44:12.835][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 05:44:12.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.841][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 05:44:12.843][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 05:44:12.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.849][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 05:44:12.851][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 05:44:12.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.857][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:44:12.859][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 05:44:12.865][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 05:44:12.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.872][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 05:44:12.874][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 05:44:12.876][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 05:44:12.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:12.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:12.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:12.885][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 05:44:12.942][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:12.982][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 05:44:12.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:12.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:44:12.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:12.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:44:12.990][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:12.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.002][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:44:13.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:44:13.009][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.011][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 05:44:13.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:44:13.014][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.015][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.017][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:44:13.017][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:44:13.017][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:44:13.017][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:44:13.017][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:44:13.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:44:13.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.022][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:44:13.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.030][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:44:13.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:44:13.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.036][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.038][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 05:44:13.041][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.042][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:44:13.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.046][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:44:13.047][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:44:13.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:44:13.057][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.059][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 05:44:13.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:44:13.062][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.063][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:44:13.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:44:13.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:44:13.065][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:44:13.065][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:44:13.067][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:44:13.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:44:13.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.078][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:44:13.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:44:13.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.083][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.085][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 05:44:13.088][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.089][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 05:44:13.091][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:44:13.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.095][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.097][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.100][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:44:13.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:44:13.103][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.105][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 05:44:13.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:44:13.109][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.111][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.112][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:44:13.115][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.122][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:44:13.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.133][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.135][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:44:13.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:44:13.141][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.143][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.149][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 05:44:13.151][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.157][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:44:13.159][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.160][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:44:13.165][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.167][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.168][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.175][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:44:13.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:44:13.182][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.183][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 05:44:13.189][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:44:13.191][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.192][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:13.198][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.199][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:44:13.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:44:13.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:13.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:13.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:44:13.222][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.223][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:44:13.229][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:44:13.231][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:13.232][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:44:13.246][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:44:13.253][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.327][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[2025-03-07 05:44:13.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.504][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 05:44:13.518][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 05:44:13.525][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 05:44:13.527][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 05:44:13.533][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:44:13.536][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 05:44:13.542][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 05:44:13.548][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 05:44:13.551][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 05:44:13.557][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 05:44:13.560][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:44:13.566][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 05:44:13.568][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 05:44:13.575][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 05:44:13.581][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 05:44:13.583][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 05:44:13.590][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 05:44:13.592][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 05:44:13.598][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:44:13.605][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 05:44:13.607][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 05:44:13.613][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 05:44:13.616][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 05:44:13.622][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 05:44:13.629][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 05:44:13.631][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 05:44:13.638][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 05:44:13.640][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 05:44:13.647][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 05:44:13.653][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 05:44:13.655][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 05:44:13.662][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 05:44:13.664][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 05:44:13.670][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 05:44:13.693][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 05:44:13.695][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 05:44:13.701][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 05:44:13.703][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 05:44:13.710][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 05:44:13.712][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 05:44:13.719][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 05:44:13.725][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 05:44:13.727][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 05:44:13.734][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 05:44:13.736][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 05:44:13.742][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 05:44:13.749][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 05:44:13.751][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 05:44:13.758][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 05:44:13.760][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 05:44:13.766][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 05:44:13.773][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 05:44:13.775][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 05:44:13.781][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 05:44:13.784][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 05:44:13.790][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 05:44:13.797][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 05:44:13.799][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 05:44:13.805][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 05:44:13.808][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 05:44:13.814][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 05:44:13.820][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 05:44:13.823][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 05:44:13.829][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 05:44:13.831][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 05:44:13.838][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 05:44:13.840][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:44:13.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:44:13.853][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 05:44:13.855][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 05:44:13.862][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 05:44:13.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 05:44:13.871][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 05:44:13.877][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 05:44:13.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 05:44:13.886][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 05:44:13.888][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 05:44:13.894][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 05:44:13.900][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 05:44:13.903][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 05:44:13.908][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 05:44:13.911][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 05:44:13.917][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 05:44:13.934][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 05:44:13.941][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:44:13.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:44:13.951][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.958][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:13.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:13.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:13.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:13.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:13.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:13.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.253][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[2025-03-07 05:44:14.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:14.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:44:14.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.334][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[2025-03-07 05:44:14.340][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 05:44:14.368][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 05:44:14.375][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:14.381][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 05:44:14.383][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:14.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:44:14.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:14.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:44:14.398][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:14.399][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 05:44:14.405][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 05:44:14.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:44:14.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:14.415][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 05:44:14.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 05:44:14.422][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 05:44:14.424][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 05:44:14.430][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:44:14.430][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:44:14.430][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:44:14.431][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 05:44:14.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:14.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:14.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:44:14.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:44:14.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:44:14.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:44:14.455][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:44:14.455][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 05:44:14.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:44:14.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:44:14.464][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 05:44:14.469][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 05:44:14.469][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 05:44:14.487][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:44:14.494][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:44:14.501][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 05:44:14.504][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:44:14.511][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:44:14.517][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:44:14.606][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 05:44:14.608][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 05:44:14.622][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 05:44:14.637][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 05:44:14.647][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:44:14.653][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:44:14.656][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 05:44:14.662][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 05:44:14.687][biodb::testThat]
biodb.INFO [2025-03-07 05:44:14.693][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-03-07 05:44:14.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:14.696][biodb::testThat]
biodb.TRACE[2025-03-07 05:44:14.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-07 05:44:14.716][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:14.729][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:14.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:14.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:14.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:14.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:14.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:14.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:14.809][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[2025-03-07 05:44:14.834][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:14.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:14.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:14.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:14.905][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:14.907][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:14.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:14.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.002][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:15.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.018][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:15.019][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:15.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:15.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.044][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:15.050][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:15.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.057][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:15.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:15.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.074][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.075][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.100][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:15.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:15.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.115][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:15.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:15.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.130][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:15.132][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.146][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.161][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:15.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:15.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:15.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:15.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.187][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:15.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:15.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:15.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:15.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.219][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:15.225][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:15.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.235][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:15.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:15.252][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:15.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:15.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:15.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:15.569][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-07 05:44:15.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:15.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:15.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:15.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:15.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:15.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:15.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:15.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.754][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:15.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:15.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:15.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:15.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.119][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.125][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:16.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:16.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:16.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:16.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:16.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:16.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.366][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:16.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:16.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:16.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:16.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:16.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:16.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:16.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:16.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.447][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:16.453][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:16.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.533][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.535][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:16.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.614][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.616][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:16.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:16.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:16.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.686][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:16.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:16.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.696][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:16.702][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:16.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.710][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:16.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.758][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.773][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.783][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.831][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.846][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.856][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.871][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.919][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:16.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:16.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:16.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:16.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:16.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:16.998][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:17.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:17.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.133][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.222][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.223][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.272][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:17.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:17.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.301][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:17.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:17.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:17.328][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:17.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:17.357][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:17.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.376][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:17.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.405][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:17.407][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:17.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.430][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:17.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:17.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:17.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:17.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.484][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 05:44:17.487][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:17.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:17.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:17.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.535][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:17.541][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:17.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.544][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 05:44:17.573][biodb::testThat]
biodb.INFO [2025-03-07 05:44:17.574][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-07 05:44:17.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:17.582][biodb::testThat]
biodb.DEBUG[2025-03-07 05:44:17.632][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-07 05:44:17.661][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:17.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-07 05:44:17.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:17.687][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-07 05:44:17.693][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:17.813][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:17.815][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:17.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:17.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:17.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:17.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:17.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:17.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:17.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:17.871][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:17.877][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:17.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:17.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.957][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:17.959][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:17.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.966][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:17.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:17.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:17.988][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:17.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:17.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:17.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:18.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.016][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:18.022][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:18.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.048][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:18.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:18.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:18.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:18.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:18.085][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:18.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.095][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:18.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.111][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:18.117][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:18.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:18.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.142][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.144][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.173][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.205][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:18.207][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:18.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.214][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.232][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:18.238][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:18.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.248][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:18.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:18.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:18.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:18.421][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-07 05:44:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-07 05:44:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-07 05:44:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-07 05:44:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-07 05:44:18.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-07 05:44:18.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-07 05:44:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:44:18.486][biodb::testThat]
biodb.INFO [2025-03-07 05:44:18.488][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-07 05:44:18.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:18.495][biodb::testThat]
biodb.TRACE[2025-03-07 05:44:18.508][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.510][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.518][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:18.519][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-07 05:44:18.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:18.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:18.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:18.671][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-07 05:44:18.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 05:44:18.751][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:18.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 05:44:18.806][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:18.808][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 05:44:18.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:18.893][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:18.895][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:44:18.902][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:18.909][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:44:18.912][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-07 05:44:18.949][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:18.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:18.959][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:18.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:18.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:18.968][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 05:44:18.982][biodb::testThat]
biodb.INFO [2025-03-07 05:44:18.984][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-03-07 05:44:18.989][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:18.991][biodb::testThat]
biodb.TRACE[2025-03-07 05:44:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:19.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:19.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:19.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:19.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:19.301][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:19.310][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:19.312][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:44:19.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:19.325][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-07 05:44:19.369][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.371][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-03-07 05:44:19.372][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:19.382][biodb::testThat]
biodb.TRACE[2025-03-07 05:44:19.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:19.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:19.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.530][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:19.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:19.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:19.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:19.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:19.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:19.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 05:44:19.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.640][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:19.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 05:44:19.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:19.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:19.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 05:44:19.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:19.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:44:19.660][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.661][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-07 05:44:19.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:19.664][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.675][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.677][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-07 05:44:19.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:19.679][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.691][biodb::testThat]
biodb.INFO [2025-03-07 05:44:19.693][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-07 05:44:19.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:19.695][biodb::testThat]
biodb.DEBUG[2025-03-07 05:44:19.701][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-07 05:44:20.864][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-07 05:44:23.032][biodb::testThat]
biodb.INFO [2025-03-07 05:44:23.034][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-07 05:44:23.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:23.041][biodb::testThat]
biodb.DEBUG[2025-03-07 05:44:23.842][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-07 05:44:24.623][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:24.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:24.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:24.629][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:24.631][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:24.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.634][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 05:44:24.637][biodb::testThat]
biodb.INFO [2025-03-07 05:44:24.638][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-03-07 05:44:24.639][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:44:24.641][biodb::testThat]
biodb.TRACE[2025-03-07 05:44:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:24.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:24.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:24.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:24.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:24.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:24.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:24.806][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:24.810][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:24.812][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:44:24.814][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:24.816][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:44:24.958][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:24.963][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:24.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:44:24.966][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:24.968][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-07 05:44:24.987][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 05:44:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 05:44:24.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:24.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:24.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:25.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:25.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:25.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:25.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:25.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:25.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:25.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:25.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:25.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:25.036][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:25.049][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:25.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 05:44:25.053][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:25.061][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 05:44:25.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:25.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:25.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:25.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:25.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:25.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:25.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:25.118][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-07 05:44:25.269][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:25.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-07 05:44:25.282][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 05:44:25.283][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 05:44:25.285][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:25.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:44:25.288][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 05:44:25.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 05:44:25.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:25.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:25.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:25.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:25.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:25.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:25.328][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[2025-03-07 05:44:25.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-07 05:44:25.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 05:44:25.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 05:44:25.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-07 05:44:28.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-07 05:44:31.387][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 05:44:31.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-07 05:44:31.443][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-07 05:44:31.451][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-07 05:44:31.458][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 05:44:31.460][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:31.466][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:31.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:31.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:31.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:31.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:31.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:31.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:31.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:31.514][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.523][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.546][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:31.547][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:31.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:31.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:31.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.571][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:31.577][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:31.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.587][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.601][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:31.603][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:31.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:31.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.627][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:31.633][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:31.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.636][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:31.659][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:31.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.700][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:31.702][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:31.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.725][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:31.726][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:31.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.734][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:31.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:31.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.750][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:31.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:31.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:31.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:31.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.776][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:31.782][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:31.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:31.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:31.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.806][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:31.807][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:31.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.815][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:31.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:31.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:31.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:31.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:31.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:31.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:31.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:31.966][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-07 05:44:31.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:31.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:32.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:32.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:32.038][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:32.047][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:32.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 05:44:32.055][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:32.065][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 05:44:32.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:32.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:32.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:32.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:32.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:32.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:32.147][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.TRACE[2025-03-07 05:44:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:32.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:32.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:32.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:32.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:32.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:32.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:32.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:32.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:32.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:32.227][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[2025-03-07 05:44:32.233][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-07 05:44:32.235][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:32.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-07 05:44:32.243][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 05:44:32.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 05:44:32.267][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:32.273][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:44:32.275][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 05:44:32.276][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 05:44:32.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:32.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:32.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:32.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:32.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:32.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:32.348][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[2025-03-07 05:44:32.354][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-07 05:44:32.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 05:44:32.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 05:44:32.456][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-07 05:44:33.213][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-07 05:44:37.959][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 05:44:37.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-07 05:44:37.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-07 05:44:37.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-07 05:44:37.978][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 05:44:37.980][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:37.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:37.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:37.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:37.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:38.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:38.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:38.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:38.018][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.020][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.040][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:38.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:38.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.055][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:38.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:38.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.071][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:38.072][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:38.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:38.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:38.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:38.103][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:38.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:38.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.133][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.157][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:38.159][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:38.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.164][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:38.166][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.171][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:38.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.177][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.179][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.216][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:38.221][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:38.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:38.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:38.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.239][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:38.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:38.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:38.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:38.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.321][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:38.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:38.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.332][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:38.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:38.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:38.422][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-07 05:44:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:38.490][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:44:38.497][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:44:38.499][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:44:38.502][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:38.504][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:44:38.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:38.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:38.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:38.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:38.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:38.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:38.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:38.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:38.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:38.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:38.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:38.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:38.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:38.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:38.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:38.573][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-07 05:44:38.575][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:38.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-07 05:44:38.582][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:38.589][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml".
biodb.DEBUG[2025-03-07 05:44:38.592][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:38.599][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:38.605][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:38.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:38.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:38.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:38.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:38.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:38.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:38.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:38.656][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.663][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.701][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:38.704][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:38.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.720][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:38.727][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:38.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.742][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:38.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:38.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.765][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:38.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.775][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:38.781][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:38.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.815][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:38.821][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.824][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:38.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.845][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:38.847][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:38.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:38.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.871][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:38.877][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:38.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.880][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:38.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.892][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:38.894][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:38.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:38.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:38.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:38.954][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-07 05:44:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:38.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:38.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:38.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:38.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:38.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:38.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:38.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:38.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:38.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:38.999][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[2025-03-07 05:44:39.001][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-07 05:44:39.002][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:39.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-07 05:44:39.006][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:39.013][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml".
biodb.DEBUG[2025-03-07 05:44:39.015][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:39.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:39.023][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:39.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:39.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:39.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:39.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:39.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:39.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:39.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:39.058][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.060][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.080][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:39.086][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:39.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.095][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:39.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:39.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.110][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:39.112][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:39.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.125][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.136][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.142][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.151][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:39.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.160][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.161][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.167][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.182][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:39.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:39.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.204][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:39.262][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-07 05:44:39.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:39.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:39.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:39.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:39.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:39.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:39.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:39.304][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[2025-03-07 05:44:39.306][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-07 05:44:39.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:39.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-07 05:44:39.311][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:39.317][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml".
biodb.DEBUG[2025-03-07 05:44:39.319][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:39.325][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:39.326][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:39.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:39.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:39.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:39.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:39.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:39.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:39.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:39.370][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.371][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.378][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.390][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:39.392][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:39.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.396][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:39.398][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:39.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.400][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:39.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:39.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.408][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.410][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.414][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.416][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.418][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.420][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:39.422][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.426][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.427][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.432][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.433][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.444][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.446][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.450][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.456][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:39.457][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:39.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:39.526][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-07 05:44:39.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:39.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:39.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:39.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:39.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:39.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:39.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:39.570][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[2025-03-07 05:44:39.571][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-07 05:44:39.573][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:39.575][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-07 05:44:39.577][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:39.585][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml".
biodb.DEBUG[2025-03-07 05:44:39.587][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:39.593][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:39.595][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:39.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:39.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:39.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:39.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:39.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:39.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:39.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:39.635][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.662][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:39.663][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:39.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.670][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:39.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.686][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:39.688][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:39.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:39.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:39.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.710][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:39.712][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:39.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:39.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:39.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:39.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.764][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.766][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.775][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:39.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.789][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:39.791][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.798][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:39.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.814][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:39.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.838][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.840][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:39.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:39.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.863][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.869][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.878][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:39.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:39.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.888][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:39.893][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:39.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.902][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:39.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:39.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:39.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:39.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:39.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.055][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-07 05:44:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:40.125][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-07 05:44:40.127][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:40.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-07 05:44:40.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:40.145][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml".
biodb.DEBUG[2025-03-07 05:44:40.147][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:40.148][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:40.150][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:40.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:40.189][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.214][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:40.215][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:40.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.238][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:40.240][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:40.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:40.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:40.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.263][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:40.264][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:40.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:40.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:40.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.287][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.293][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.311][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.316][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.335][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:40.341][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:40.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.359][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.383][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:40.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:40.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:40.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:40.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.408][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:40.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:40.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.422][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:40.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.448][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:40.454][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:40.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.463][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:40.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:40.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.550][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-07 05:44:40.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.581][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.DEBUG[2025-03-07 05:44:40.582][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-07 05:44:40.584][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:40.586][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-07 05:44:40.588][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:40.597][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml".
biodb.DEBUG[2025-03-07 05:44:40.599][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:40.601][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:40.603][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:40.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:40.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.646][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.652][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.661][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:40.663][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:40.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.669][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:40.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:40.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.695][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:40.699][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:40.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:40.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:40.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.711][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:40.712][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:40.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:40.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:40.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.723][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:40.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.736][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.738][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:40.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.743][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:40.744][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.747][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:40.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.769][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.783][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:40.784][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:40.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:40.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:40.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.795][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:40.796][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:40.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.801][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:40.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.815][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:40.817][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:40.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:40.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:40.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.902][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-07 05:44:40.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:40.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:40.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:40.936][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-07 05:44:40.937][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:40.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-07 05:44:40.941][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:40.949][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml".
biodb.DEBUG[2025-03-07 05:44:40.951][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:40.953][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:40.954][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:40.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:40.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:40.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:40.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:40.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:40.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:40.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:40.983][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.985][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:40.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:40.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:40.996][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:40.998][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:40.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.002][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.013][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.015][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.039][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.045][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.057][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.059][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.075][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.077][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.080][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.082][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.090][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.101][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.102][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.113][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.115][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.135][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.136][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.237][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-07 05:44:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:41.274][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-07 05:44:41.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:41.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-07 05:44:41.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:41.283][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml".
biodb.DEBUG[2025-03-07 05:44:41.285][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:41.287][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:41.289][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:41.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:41.317][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.343][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.349][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.373][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.375][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.379][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.390][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.392][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.400][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.401][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.412][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.413][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.418][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.424][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.432][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.442][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.444][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.461][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.475][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.477][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.548][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-07 05:44:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:41.582][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-07 05:44:41.583][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:41.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-07 05:44:41.587][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:41.591][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml".
biodb.DEBUG[2025-03-07 05:44:41.593][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:41.594][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:41.596][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:41.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:41.617][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.630][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.632][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.637][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.644][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.648][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.657][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.658][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.670][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.682][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.684][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.686][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.692][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.698][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.699][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.711][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.722][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.723][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.728][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.742][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.743][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.748][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:41.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.812][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-07 05:44:41.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:41.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:41.844][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-07 05:44:41.845][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:41.847][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-07 05:44:41.849][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:41.852][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml".
biodb.DEBUG[2025-03-07 05:44:41.853][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:41.855][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:41.856][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:41.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:41.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:41.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:41.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:41.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:41.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:41.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:41.874][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.876][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:41.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:41.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.886][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.887][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.892][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:41.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:41.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.898][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.899][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:41.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:41.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:41.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.921][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.922][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:41.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.933][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.934][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:41.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.939][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.944][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:41.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:41.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.950][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.954][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.961][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.966][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:41.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:41.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.973][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.975][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.978][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:41.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:41.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.993][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:41.994][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:41.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:41.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:42.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:42.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.061][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-07 05:44:42.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.091][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[2025-03-07 05:44:42.092][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-07 05:44:42.094][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:42.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-07 05:44:42.097][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:42.100][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2025-03-07 05:44:42.102][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:42.103][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:42.105][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:42.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:42.123][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.124][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.134][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.145][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.147][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.157][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:42.158][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:42.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.162][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.164][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.168][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.169][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.174][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.196][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.207][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.209][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.213][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.219][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:42.220][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:42.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.323][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-07 05:44:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:42.354][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-07 05:44:42.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:42.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-07 05:44:42.360][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:42.362][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2025-03-07 05:44:42.364][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:42.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:42.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:42.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:42.385][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.396][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.398][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.400][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.407][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.419][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:42.420][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:42.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.425][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.426][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.429][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.430][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.436][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.438][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.440][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.442][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.451][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.452][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.464][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.479][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.480][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.485][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.491][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:42.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:42.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.638][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-07 05:44:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:42.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:42.717][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-07 05:44:42.718][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:42.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-07 05:44:42.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:42.745][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2025-03-07 05:44:42.747][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:42.754][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:42.756][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:42.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:42.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:42.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:42.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:42.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:42.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:42.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:42.801][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.803][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.827][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.829][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.831][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.838][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:42.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:42.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.848][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.876][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:42.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:42.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:42.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:42.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.897][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.898][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:42.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.909][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.911][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:42.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.915][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.917][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.921][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:42.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:42.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.927][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.929][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:42.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.939][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.944][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:42.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.952][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.953][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:42.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:42.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.964][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:42.966][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:42.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.971][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:42.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:42.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:42.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:42.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:42.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:42.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:42.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.042][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-07 05:44:43.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:43.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:43.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:43.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:43.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:43.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:43.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:43.078][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-07 05:44:43.079][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:43.081][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-07 05:44:43.083][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:43.088][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2025-03-07 05:44:43.090][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:43.092][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:43.101][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:43.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:43.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:43.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:43.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:43.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:43.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:43.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:43.119][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.121][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.131][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:43.132][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:43.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.137][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:43.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:43.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.143][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:43.144][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:43.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.147][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:43.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:43.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.155][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:43.156][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:43.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:43.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.180][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:43.182][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:43.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.185][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.186][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:43.188][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.192][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:43.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.200][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.203][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.210][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:43.212][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:43.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:43.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:43.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.223][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:43.224][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:43.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.229][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:43.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:43.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.235][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:43.236][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:43.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.239][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.315][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-07 05:44:43.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:43.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:43.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:43.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:43.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:43.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:43.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:43.386][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-07 05:44:43.388][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:43.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-07 05:44:43.409][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:43.415][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2025-03-07 05:44:43.417][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:43.418][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:43.420][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:43.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:43.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:43.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:43.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:43.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:43.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:43.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:43.447][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.490][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:43.491][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:43.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.499][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:43.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:43.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.515][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:43.521][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:43.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:43.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.545][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:43.547][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:43.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:43.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:43.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.567][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.570][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:43.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.578][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:43.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:43.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.589][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:43.591][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.596][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:43.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.607][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.615][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:43.617][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:43.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:43.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.628][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:43.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:43.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:43.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:43.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:43.643][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:43.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:43.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:43.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.867][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-07 05:44:43.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:43.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:43.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:43.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:43.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:43.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:43.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:44.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:44.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:44.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:44.014][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-07 05:44:44.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:44.257][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-07 05:44:44.289][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:44.749][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2025-03-07 05:44:59.137][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:59.175][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:59.178][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:59.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:59.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:59.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:59.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:59.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:59.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:59.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:59.285][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.313][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:59.315][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:59.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:59.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:59.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.355][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:59.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:59.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:59.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.397][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:59.400][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:59.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:59.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:59.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.419][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.436][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:59.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:59.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.446][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:59.448][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.453][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:59.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.464][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.478][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:59.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:59.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:59.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:59.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.511][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:59.513][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:59.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:59.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.527][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:59.529][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:59.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:59.644][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-07 05:44:59.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:44:59.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:59.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:59.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:59.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:59.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:59.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:59.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:44:59.696][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-07 05:44:59.698][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:44:59.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-07 05:44:59.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:44:59.766][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2025-03-07 05:44:59.768][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:44:59.770][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:44:59.791][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:44:59.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:44:59.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:44:59.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:44:59.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:44:59.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:44:59.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:44:59.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:44:59.815][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.816][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.830][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:59.831][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:59.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.834][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:44:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:44:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.841][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:59.843][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:59.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:44:59.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:44:59.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:59.862][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:59.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:44:59.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:44:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.872][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.874][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:44:59.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:59.886][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:44:59.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.890][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:59.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.896][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:44:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:44:59.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.901][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.903][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.905][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:44:59.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.913][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:59.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:59.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:44:59.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:44:59.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.924][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:59.926][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:59.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.928][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:44:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:44:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.936][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:59.938][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:59.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.940][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:44:59.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:44:59.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:44:59.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:44:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:44:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:44:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:44:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:00.048][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-07 05:45:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:00.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:00.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:00.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:00.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:00.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:00.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:00.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:45:00.081][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-07 05:45:00.083][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:45:00.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-07 05:45:00.087][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:00.101][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2025-03-07 05:45:00.103][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:45:00.109][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:45:00.111][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:45:00.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:00.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:00.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:00.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:00.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:00.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:00.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:00.157][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.183][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:00.184][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:00.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:00.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.213][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:00.215][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:00.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:00.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:00.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.240][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:00.246][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:00.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.271][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:00.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:00.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:00.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:00.304][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:00.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.311][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.317][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:00.319][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.333][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.344][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:00.350][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:00.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.358][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:00.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:00.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.376][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:00.382][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:00.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:00.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.413][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:00.415][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:00.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:00.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:00.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.445][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:00.447][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:00.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.462][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:00.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:00.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:00.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:00.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:00.628][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-07 05:45:00.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:00.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:00.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:00.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:00.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:00.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:04.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:04.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:04.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:04.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:45:04.950][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-07 05:45:04.951][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:45:04.956][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-07 05:45:04.960][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:12.187][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2025-03-07 05:45:12.223][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:45:12.230][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:45:12.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:45:12.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:12.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:12.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:12.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:12.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:12.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:12.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:12.402][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.404][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.417][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:12.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:12.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.423][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:12.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:12.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.455][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:12.466][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:12.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.486][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:12.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:12.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.520][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:12.531][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:12.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:12.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:12.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:12.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.591][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:12.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.624][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:12.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:12.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.638][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.640][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:12.650][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.663][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:12.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:12.685][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:12.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:12.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.710][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:12.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:12.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:12.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:12.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.728][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:12.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:12.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.732][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.734][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:12.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:12.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.741][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:12.743][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:12.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:12.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:12.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:12.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:12.847][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-07 05:45:12.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:12.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:12.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:12.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:12.938][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:45:12.953][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:45:12.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:45:12.957][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:12.961][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:45:12.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:12.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:12.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:12.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:12.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:12.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:12.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.186][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[2025-03-07 05:45:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:13.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:13.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:13.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:13.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:13.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:13.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:13.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:13.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:13.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:14.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:15.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:16.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:21.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.193][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[2025-03-07 05:45:24.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:24.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:24.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:24.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:24.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:24.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:24.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:24.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:24.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:24.807][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[2025-03-07 05:45:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:24.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:24.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:24.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:45:25.033][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:45:25.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2025-03-07 05:45:25.042][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:25.057][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2025-03-07 05:45:25.066][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:45:25.076][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:45:25.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2025-03-07 05:45:25.084][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:25.101][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2025-03-07 05:45:25.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:25.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:25.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:25.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:25.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:25.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:25.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:45:25.152][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-07 05:45:25.158][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:45:25.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-07 05:45:25.177][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:25.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2025-03-07 05:45:25.187][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:45:25.202][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:45:25.209][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:45:25.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:25.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:25.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:25.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:25.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:25.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:25.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:25.259][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:25.265][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:25.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:25.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:25.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:25.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:25.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:25.290][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:25.292][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:25.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:25.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:25.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:25.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:25.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:25.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:25.368][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:25.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:25.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:25.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:25.425][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:36.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:36.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:36.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:36.867][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:36.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:36.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:36.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:36.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:36.940][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:36.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:36.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:36.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:36.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:36.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:36.979][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:36.981][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:36.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:36.984][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.057][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:37.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:37.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.064][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:37.066][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:37.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.075][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:37.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:37.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.121][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:37.123][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:37.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:37.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:37.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.148][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:37.154][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:37.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.163][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:37.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:37.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:37.179][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:37.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:37.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:37.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:37.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:37.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:37.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:37.274][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-07 05:45:37.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:37.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:37.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:37.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:37.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:37.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:37.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:40.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:40.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:40.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:40.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:40.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:40.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:40.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:40.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:40.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:40.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:40.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:40.316][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[2025-03-07 05:45:40.318][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-07 05:45:40.325][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:45:40.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-07 05:45:40.457][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:40.553][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2025-03-07 05:45:40.556][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:45:40.563][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:45:40.565][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:45:40.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:40.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:40.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:40.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:40.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:40.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:40.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:40.621][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:40.623][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:40.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:40.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:40.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.644][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:40.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:40.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:45:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:45:40.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.732][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:40.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:40.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:45:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:45:40.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.744][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:40.746][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:40.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:45:40.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:45:40.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:40.774][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:40.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.777][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:45:40.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:45:40.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.785][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:40.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:45:40.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.792][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:40.794][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:40.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.797][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.802][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:45:40.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:45:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:40.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.831][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:40.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:40.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:45:40.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:45:40.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:40.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:40.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:40.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:40.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:45:41.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:45:42.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.214][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:42.218][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:42.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.268][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:45:42.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:45:42.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:45:42.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:45:42.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:45:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:42.416][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-07 05:45:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:42.541][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:45:42.607][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:45:42.610][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:45:42.611][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:42.675][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:45:42.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:42.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:42.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:42.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:42.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:42.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:42.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:42.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:42.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:42.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:42.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:42.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:42.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:42.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:42.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:42.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:42.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:42.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:42.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:42.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:42.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:42.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:42.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:42.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:42.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:42.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:42.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:42.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:42.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:42.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:42.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:42.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:42.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:42.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:42.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.261][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[2025-03-07 05:45:43.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.424][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[2025-03-07 05:45:43.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.872][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[2025-03-07 05:45:43.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:43.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:43.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:43.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:43.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:43.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:43.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:43.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:43.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:44.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:44.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:44.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:44.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:44.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:44.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:44.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:44.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:44.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:44.187][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:45:46.364][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:45:46.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 05:45:46.380][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:45:46.386][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 05:45:46.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.687][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.TRACE[2025-03-07 05:45:46.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:46.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:46.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:46.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:46.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:46.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:46.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:46.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:46.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:46.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:46.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:56.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:56.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:56.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:56.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:56.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:56.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:56.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:45:56.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:45:56.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:45:56.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:45:56.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:45:56.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:45:56.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:45:57.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:45:57.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:45:57.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:45:57.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:57.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:45:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.631][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.TRACE[2025-03-07 05:46:00.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.764][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[2025-03-07 05:46:00.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:00.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:00.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:00.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:00.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:00.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:00.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:00.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:00.984][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[2025-03-07 05:46:00.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:00.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:00.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:01.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:01.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:01.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:01.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:01.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:02.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:46:02.209][biodb::testThat]
biodb.INFO [2025-03-07 05:46:02.210][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-07 05:46:02.212][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:02.222][biodb::testThat]
biodb.TRACE[2025-03-07 05:46:02.265][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 05:46:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 05:46:02.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:02.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.335][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[2025-03-07 05:46:02.340][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:02.377][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:02.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 05:46:02.386][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:02.451][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 05:46:02.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.555][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[2025-03-07 05:46:02.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:02.593][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:02.607][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:02.609][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 05:46:02.611][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:02.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 05:46:02.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:02.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:02.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.687][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.TRACE[2025-03-07 05:46:02.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:02.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:02.705][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:02.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:02.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.735][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.736][private$selectFields]
biodb.TRACE[2025-03-07 05:46:02.737][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:02.738][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:02.740][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.742][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.756][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.760][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:02.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.793][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 05:46:02.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:02.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.830][private$selectFields]
biodb.TRACE[2025-03-07 05:46:02.832][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:02.834][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:02.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.866][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.868][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.869][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.874][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.876][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:02.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.898][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:02.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:02.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:02.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:02.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:02.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:02.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:02.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:02.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.950][private$selectFields]
biodb.TRACE[2025-03-07 05:46:02.952][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:02.953][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:02.955][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.957][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.962][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.970][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.972][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:02.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:02.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:02.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.979][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:02.987][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.601][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:10.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:10.662][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:10.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:10.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:10.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:10.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:10.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:10.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:10.690][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 05:46:10.691][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:10.693][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:12.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:12.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:12.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:12.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:12.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:12.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:13.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:13.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:13.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:13.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:13.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:13.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:13.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:13.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:14.140][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:14.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 05:46:14.160][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:14.169][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 05:46:14.192][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:14.199][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:14.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 05:46:14.203][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:14.209][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 05:46:14.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:14.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:14.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.283][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.TRACE[2025-03-07 05:46:14.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:14.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:14.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:14.367][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:14.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:14.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.436][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.438][private$selectFields]
biodb.TRACE[2025-03-07 05:46:14.439][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:14.440][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:14.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.443][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.450][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.454][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.455][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.457][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.462][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.481][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 05:46:14.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.558][private$selectFields]
biodb.TRACE[2025-03-07 05:46:14.559][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:14.560][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:14.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.568][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.573][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.574][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.589][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.595][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.597][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.615][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:14.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:14.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:14.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:14.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:14.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:14.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:14.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.671][private$selectFields]
biodb.TRACE[2025-03-07 05:46:14.673][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:14.675][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:14.676][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.678][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.680][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.683][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.691][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.692][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:14.694][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.695][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.699][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:14.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:14.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:14.720][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 05:46:14.722][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:14.723][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:15.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:46:15.274][biodb::testThat]
biodb.INFO [2025-03-07 05:46:15.275][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-07 05:46:15.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:15.286][biodb::testThat]
biodb.TRACE[2025-03-07 05:46:15.298][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 05:46:15.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 05:46:15.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:15.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:15.355][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:15.386][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:15.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 05:46:15.390][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:15.401][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 05:46:15.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:15.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:15.459][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:15.465][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:15.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 05:46:15.469][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:15.472][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 05:46:15.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:15.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:15.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:15.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:15.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:15.566][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:15.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.582][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.TRACE[2025-03-07 05:46:15.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.628][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.630][private$selectFields]
biodb.TRACE[2025-03-07 05:46:15.631][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:15.633][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:15.634][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.637][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.640][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.642][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.643][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.649][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.651][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.657][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:15.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.678][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 05:46:15.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.708][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.710][private$selectFields]
biodb.TRACE[2025-03-07 05:46:15.711][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:15.718][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:15.720][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.723][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.732][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.737][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.739][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.748][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:15.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.772][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:15.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.809][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.810][private$selectFields]
biodb.TRACE[2025-03-07 05:46:15.830][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:15.832][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:15.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.845][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.847][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.854][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:15.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.862][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.864][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:15.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:15.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.888][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 05:46:15.889][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:15.891][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:15.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:15.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:15.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:15.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:15.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:15.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:15.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:15.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:15.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:15.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:15.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:15.955][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:15.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:15.972][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 05:46:15.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:15.979][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 05:46:16.032][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:16.040][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:16.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 05:46:16.044][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:16.048][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 05:46:16.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:16.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.250][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.254][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.TRACE[2025-03-07 05:46:16.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:16.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:16.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:16.328][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:16.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.344][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[2025-03-07 05:46:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.373][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.375][private$selectFields]
biodb.TRACE[2025-03-07 05:46:16.376][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:16.378][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:16.379][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.381][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.383][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.385][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.393][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.396][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.404][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.424][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 05:46:16.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.455][private$selectFields]
biodb.TRACE[2025-03-07 05:46:16.456][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:16.458][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:16.459][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.467][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.468][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.472][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.474][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.477][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.481][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.500][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:16.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:16.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.529][private$selectFields]
biodb.TRACE[2025-03-07 05:46:16.530][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:16.531][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:16.533][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.534][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.542][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.546][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:16.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.550][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.555][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:16.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.576][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 05:46:16.577][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:16.579][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:46:16.606][biodb::testThat]
biodb.INFO [2025-03-07 05:46:16.607][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-07 05:46:16.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:16.610][biodb::testThat]
biodb.TRACE[2025-03-07 05:46:16.617][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 05:46:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 05:46:16.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:16.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:16.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:16.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:16.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:16.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:16.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:16.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:16.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:16.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:16.689][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[2025-03-07 05:46:16.704][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:16.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:16.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 05:46:16.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:16.766][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 05:46:16.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:17.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:17.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:17.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:17.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:17.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:23.164][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:23.175][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:23.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 05:46:23.179][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:23.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 05:46:23.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:23.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:23.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:23.277][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:23.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.315][private$selectFields]
biodb.TRACE[2025-03-07 05:46:23.317][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:23.319][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:23.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.323][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.329][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.332][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.340][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.341][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.347][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.349][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:23.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.390][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 05:46:23.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.421][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.422][private$selectFields]
biodb.TRACE[2025-03-07 05:46:23.424][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:23.425][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:23.427][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.428][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.435][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.440][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.443][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.444][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.451][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:23.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.472][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:23.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:23.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.503][private$selectFields]
biodb.TRACE[2025-03-07 05:46:23.505][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:23.506][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:23.507][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.515][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.517][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.521][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.522][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:23.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.530][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:23.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:23.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.550][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 05:46:23.552][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:23.553][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:23.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:23.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:23.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:23.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:23.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:23.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:23.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:23.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:23.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:23.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:23.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:23.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:23.705][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:23.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 05:46:26.201][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:26.287][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 05:46:26.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:26.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:26.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 05:46:26.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:26.320][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 05:46:26.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:26.339][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[2025-03-07 05:46:26.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:26.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:26.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:26.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:26.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:26.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:26.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:26.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:26.423][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 05:46:26.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:26.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:26.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.452][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.453][private$selectFields]
biodb.TRACE[2025-03-07 05:46:26.454][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:26.456][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:26.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.464][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.466][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.468][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.471][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.478][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:26.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.498][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 05:46:26.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:26.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:26.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.535][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.536][private$selectFields]
biodb.TRACE[2025-03-07 05:46:26.537][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:26.539][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:26.540][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.542][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.547][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.549][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:26.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.577][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:26.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:26.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:26.673][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 05:46:26.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:26.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:26.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:26.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:26.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:26.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:27.005][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[2025-03-07 05:46:27.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.551][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:27.552][private$selectFields]
biodb.TRACE[2025-03-07 05:46:27.554][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 05:46:27.555][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 05:46:27.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:27.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.568][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:27.569][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 05:46:27.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 05:46:27.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.593][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 05:46:27.595][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 05:46:27.596][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 05:46:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 05:46:27.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 05:46:27.632][biodb::testThat]
biodb.INFO [2025-03-07 05:46:27.634][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-03-07 05:46:27.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:27.636][biodb::testThat]
biodb.DEBUG[2025-03-07 05:46:27.639][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-07 05:46:27.640][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:46:27.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-07 05:46:27.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:27.668][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2025-03-07 05:46:27.671][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:46:27.673][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:46:27.675][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:46:27.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:27.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:27.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:27.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:27.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:27.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:27.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:27.704][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.724][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:27.726][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:27.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.731][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:27.733][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:27.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.739][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:27.741][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:27.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.744][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.746][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:27.747][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:27.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.752][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:27.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:27.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.759][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:27.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:27.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:27.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:27.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.773][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:27.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:27.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.780][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:27.782][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:27.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.804][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:27.807][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:27.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:27.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:27.875][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-07 05:46:27.877][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-07 05:46:27.889][biodb::testThat]
biodb.INFO [2025-03-07 05:46:27.891][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-07 05:46:27.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:27.893][biodb::testThat]
biodb.DEBUG[2025-03-07 05:46:27.914][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-07 05:46:27.916][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-07 05:46:27.918][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-07 05:46:27.920][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-07 05:46:27.922][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-03-07 05:46:27.926][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2025-03-07 05:46:27.928][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:46:27.930][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-07 05:46:27.932][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-07 05:46:27.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:27.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:27.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:27.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:27.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:27.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:27.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:27.960][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:27.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:27.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.975][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:27.976][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:27.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.986][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:27.988][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:27.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:27.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:27.999][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:28.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:28.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.006][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.007][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.012][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.013][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.018][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:28.019][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:28.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.024][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.025][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.029][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:28.031][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:28.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.035][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:28.037][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:28.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.042][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:28.044][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:28.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:28.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:28.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:28.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:28.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:28.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:28.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:28.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:46:28.128][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.130][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.139][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:28.141][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:28.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:28.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:28.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.150][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:28.152][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:28.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:28.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:28.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.165][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:28.167][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:28.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.169][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:28.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:28.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.177][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.189][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.190][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.200][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:28.202][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:28.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.204][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.206][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:28.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:28.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.212][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.223][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:28.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:28.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:28.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:28.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.241][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:28.242][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:28.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.250][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:28.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:28.257][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:28.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:28.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:28.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:46:28.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:28.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:28.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:28.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:28.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:28.322][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.TRACE[2025-03-07 05:46:28.328][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.332][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.344][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:28.345][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:28.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.353][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:46:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:46:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.358][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:28.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:28.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.363][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:46:28.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:46:28.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.379][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:28.381][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:28.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.384][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:46:28.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:46:28.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.395][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.396][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.399][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:46:28.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.412][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.424][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:46:28.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.431][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:28.432][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:28.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.443][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:46:28.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:46:28.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.449][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:28.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.469][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:28.471][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:28.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:28.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:28.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:28.494][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:28.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.503][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:46:28.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:46:28.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.511][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:28.513][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:28.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:46:28.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:46:28.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:46:28.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:46:28.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:46:28.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:28.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:46:40.246][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-07 05:46:40.278][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-07 05:46:40.282][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-07 05:46:40.395][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.397][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-03-07 05:46:40.399][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:40.402][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.581][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.583][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-03-07 05:46:40.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:40.586][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.600][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.602][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-03-07 05:46:40.603][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:40.605][biodb::testThat]
biodb.DEBUG[2025-03-07 05:46:40.609][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:46:40.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:46:40.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2025-03-07 05:46:40.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:46:40.669][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2025-03-07 05:46:40.753][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:46:40.755][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:46:40.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:40.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:46:40.763][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:40.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:46:40.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:46:40.770][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 05:46:40.773][biodb::testThat]
biodb.INFO [2025-03-07 05:46:40.775][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-07 05:46:40.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:46:40.778][biodb::testThat]
biodb.ERROR[2025-03-07 05:46:40.851][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-07 05:46:40.971][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-07 05:46:40.995][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 05:46:41.002][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 05:46:41.004][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 05:46:41.005][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 05:46:41.007][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:41.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:41.010][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:41.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:41.012][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:41.014][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.INFO [2025-03-07 05:46:42.143][biodb::testContext]
biodb.INFO [2025-03-07 05:46:42.181][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:46:42.183][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-07 05:46:42.202][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:46:42.203][biodb::testContext]
biodb.INFO [2025-03-07 05:46:44.026][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:46:44.101][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 05:46:44.142][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:46:44.144][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 05:46:44.147][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.154][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 05:46:44.155][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.166][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 05:46:44.168][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.188][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 05:46:44.190][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 05:46:44.192][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 05:46:44.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.211][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 05:46:44.212][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 05:46:44.222][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.233][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 05:46:44.235][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 05:46:44.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.251][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 05:46:44.257][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 05:46:44.259][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 05:46:44.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.274][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 05:46:44.314][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.323][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 05:46:44.325][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 05:46:44.327][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 05:46:44.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.332][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:46:44.334][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 05:46:44.335][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 05:46:44.337][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 05:46:44.339][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 05:46:44.340][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 05:46:44.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.344][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[2025-03-07 05:46:44.346][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 05:46:44.347][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 05:46:44.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.353][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 05:46:44.354][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 05:46:44.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.358][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[2025-03-07 05:46:44.359][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 05:46:44.361][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 05:46:44.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.366][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 05:46:44.368][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 05:46:44.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.373][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 05:46:44.375][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 05:46:44.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.380][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:46:44.382][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 05:46:44.461][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 05:46:44.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.467][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 05:46:44.469][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 05:46:44.470][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 05:46:44.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.476][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 05:46:44.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.480][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 05:46:44.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:46:44.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.490][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:46:44.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:46:44.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.495][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 05:46:44.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:46:44.498][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.499][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.500][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:46:44.500][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:46:44.500][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:46:44.500][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:46:44.500][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:46:44.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:46:44.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.506][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:46:44.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.511][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:46:44.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:46:44.515][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.517][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.519][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 05:46:44.521][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.523][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:46:44.524][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:46:44.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.532][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.533][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:46:44.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:46:44.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.538][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 05:46:44.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:46:44.540][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.543][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:46:44.543][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:46:44.543][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:46:44.543][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:46:44.543][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:46:44.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:46:44.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:46:44.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.555][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:46:44.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:46:44.559][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.560][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.562][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 05:46:44.565][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.566][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 05:46:44.568][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.569][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:46:44.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.572][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.573][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.575][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.576][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:46:44.577][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:46:44.579][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.580][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 05:46:44.582][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:46:44.583][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.584][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.586][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.587][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:46:44.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.591][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:46:44.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.597][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:46:44.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:46:44.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.602][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.604][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 05:46:44.606][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.608][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:46:44.609][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.611][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:46:44.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.615][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.618][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:46:44.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:46:44.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.623][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 05:46:44.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:46:44.626][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.627][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:46:44.629][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:46:44.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:46:44.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:46:44.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:46:44.649][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:46:44.651][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.652][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:46:44.653][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:46:44.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:46:44.656][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:46:44.658][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:46:44.659][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.661][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[2025-03-07 05:46:44.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.667][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[2025-03-07 05:46:44.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.719][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[2025-03-07 05:46:44.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.745][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[2025-03-07 05:46:44.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.752][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[2025-03-07 05:46:44.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.775][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 05:46:44.777][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 05:46:44.780][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 05:46:44.782][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 05:46:44.785][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:46:44.787][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 05:46:44.789][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 05:46:44.791][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 05:46:44.793][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 05:46:44.795][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 05:46:44.797][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:46:44.799][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 05:46:44.801][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 05:46:44.803][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 05:46:44.805][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 05:46:44.807][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 05:46:44.809][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 05:46:44.811][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 05:46:44.814][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:46:44.816][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 05:46:44.818][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 05:46:44.820][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 05:46:44.822][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 05:46:44.825][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 05:46:44.828][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 05:46:44.830][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 05:46:44.832][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 05:46:44.835][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 05:46:44.837][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 05:46:44.840][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 05:46:44.843][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 05:46:44.846][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 05:46:44.848][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 05:46:44.851][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 05:46:44.854][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 05:46:44.856][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 05:46:44.859][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 05:46:44.862][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 05:46:44.864][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 05:46:44.867][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 05:46:44.869][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 05:46:44.872][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 05:46:44.875][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 05:46:44.878][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 05:46:44.880][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 05:46:44.883][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 05:46:44.885][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 05:46:44.888][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 05:46:44.901][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 05:46:44.904][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 05:46:44.907][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 05:46:44.909][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 05:46:44.911][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 05:46:44.914][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 05:46:44.916][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 05:46:44.919][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 05:46:44.921][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 05:46:44.924][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 05:46:44.926][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 05:46:44.928][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 05:46:44.931][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 05:46:44.933][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 05:46:44.936][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 05:46:44.939][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 05:46:44.941][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 05:46:44.944][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 05:46:44.946][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:46:44.948][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:46:44.950][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 05:46:44.953][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 05:46:44.955][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 05:46:44.958][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 05:46:44.961][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 05:46:44.963][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 05:46:44.966][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 05:46:44.969][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 05:46:44.972][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 05:46:44.975][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 05:46:44.977][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 05:46:44.980][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 05:46:44.982][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 05:46:44.984][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 05:46:44.986][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 05:46:44.988][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 05:46:44.990][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:46:44.992][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:46:44.993][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:44.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:44.995][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:44.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:44.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:44.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.005][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[2025-03-07 05:46:45.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:45.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:45.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:45.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:45.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:45.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:45.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:45.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:48.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:51.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:51.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:51.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:51.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:51.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:51.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:51.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:51.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:51.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:51.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:51.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:46:51.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:46:51.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:46:51.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:46:51.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:46:51.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:46:51.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:46:51.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.328][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[2025-03-07 05:48:55.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:48:55.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:48:55.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:48:55.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:48:55.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:48:55.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:48:55.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:48:55.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:48:55.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:48:55.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:48:55.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:48:56.355][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 05:48:56.557][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 05:48:56.571][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:48:56.573][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 05:48:56.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:48:56.576][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:48:56.578][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:48:56.580][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:48:56.581][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 05:48:56.583][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 05:48:56.584][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 05:48:56.586][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:48:56.588][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:48:56.590][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 05:48:56.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 05:48:56.593][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 05:48:56.595][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 05:48:56.597][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:48:56.597][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:48:56.597][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:48:56.599][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 05:48:56.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:48:56.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:48:56.604][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:48:56.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:48:56.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:48:56.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:48:56.612][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:48:56.612][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 05:48:56.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:48:56.615][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:48:56.617][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 05:48:56.618][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 05:48:56.618][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 05:48:56.621][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:48:56.624][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:48:56.626][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 05:48:56.629][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:48:56.631][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:48:56.634][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:48:56.648][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 05:48:56.650][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 05:48:56.652][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 05:48:56.668][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 05:48:56.670][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:48:56.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:48:56.678][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 05:48:56.680][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 05:48:56.685][biodb::testThat]
biodb.INFO [2025-03-07 05:48:56.686][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-03-07 05:48:56.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:48:56.690][biodb::testThat]
biodb.DEBUG[2025-03-07 05:48:56.698][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 05:48:56.757][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:48:56.804][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 05:49:06.133][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.176][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 05:49:06.206][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.229][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 05:49:06.235][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.238][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 05:49:06.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.322][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[2025-03-07 05:49:06.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 05:49:06.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.346][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 05:49:06.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.434][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 05:49:06.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.443][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 05:49:06.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.490][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.499][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.502][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 05:49:06.505][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.512][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 05:49:06.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.609][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.620][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 05:49:06.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.625][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 05:49:06.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.654][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.656][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 05:49:06.658][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.660][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 05:49:06.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.678][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[2025-03-07 05:49:06.681][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.693][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2025-03-07 05:49:06.705][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2025-03-07 05:49:06.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.747][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.INFO [2025-03-07 05:49:06.760][biodb::testThat]
biodb.INFO [2025-03-07 05:49:06.762][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-03-07 05:49:06.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:49:06.764][biodb::testThat]
biodb.DEBUG[2025-03-07 05:49:06.769][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:06.802][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:06.804][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2025-03-07 05:49:06.806][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:06.825][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2025-03-07 05:49:06.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:06.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:06.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:06.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:06.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:06.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:06.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:06.979][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:49:07.169][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:49:07.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2025-03-07 05:49:07.292][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:49:07.328][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2025-03-07 05:49:07.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:49:07.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:07.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:07.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:07.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:07.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 05:49:07.422][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 05:49:07.424][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 05:49:07.425][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 05:49:07.426][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 05:49:07.428][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:49:07.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:49:07.430][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:49:07.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:49:07.433][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 05:49:07.471][biodb::testContext]
biodb.INFO [2025-03-07 05:49:07.473][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:49:07.474][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-07 05:49:07.476][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:49:07.477][biodb::testContext]
biodb.INFO [2025-03-07 05:49:07.561][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:49:07.567][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 05:49:07.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:49:07.593][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 05:49:07.596][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.602][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 05:49:07.604][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.607][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[2025-03-07 05:49:07.609][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 05:49:07.610][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.615][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 05:49:07.617][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 05:49:07.618][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 05:49:07.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.623][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 05:49:07.625][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 05:49:07.626][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.631][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 05:49:07.633][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 05:49:07.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.638][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 05:49:07.639][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 05:49:07.641][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 05:49:07.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.646][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 05:49:07.648][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.653][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 05:49:07.654][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 05:49:07.656][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 05:49:07.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.661][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:49:07.663][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 05:49:07.664][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 05:49:07.666][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 05:49:07.667][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 05:49:07.669][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 05:49:07.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.674][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 05:49:07.676][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 05:49:07.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.681][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 05:49:07.683][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 05:49:07.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.688][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 05:49:07.690][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 05:49:07.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:49:07.695][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 05:49:07.697][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 05:49:07.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:49:07.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:49:07.701][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[2025-03-07 05:49:07.720][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 05:49:18.673][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 05:49:18.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:09.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:09.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:09.555][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:50:09.560][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 05:50:16.574][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 05:50:16.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:16.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:16.835][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 05:50:16.837][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 05:50:16.839][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 05:50:16.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:16.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:16.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:16.846][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 05:50:16.849][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:16.851][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 05:50:16.853][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:16.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:16.860][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:16.862][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:16.863][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:50:16.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:16.867][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.873][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 05:50:16.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:16.881][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:16.883][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.889][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:16.889][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:16.889][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:16.889][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:50:16.889][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:50:16.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:16.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:16.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:16.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:16.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:16.922][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:16.923][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:16.925][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:16.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:16.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:16.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:16.931][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:16.933][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 05:50:16.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:16.938][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:50:16.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:16.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:16.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:16.947][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:16.948][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:16.950][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:50:16.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:16.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:17.334][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 05:50:17.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:17.362][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:17.366][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:17.367][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:17.367][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:17.367][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:17.367][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:50:17.367][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:50:17.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:17.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:17.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:17.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:17.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:17.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:17.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:17.382][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:17.383][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:17.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:17.386][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:17.388][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:17.389][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 05:50:17.392][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:17.394][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 05:50:17.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:17.398][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:17.399][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:17.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.141][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.144][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:50:19.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:19.147][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.148][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 05:50:19.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:19.151][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.152][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:19.154][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:19.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:19.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:19.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:19.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:19.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:19.163][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.164][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.165][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:19.167][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:19.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.169][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.171][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 05:50:19.173][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:19.175][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:50:19.176][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:19.177][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:19.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:19.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.181][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.184][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:50:19.186][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:19.187][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.189][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 05:50:19.190][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:19.192][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.197][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:19.199][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:19.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:19.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:19.216][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:19.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:19.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:19.220][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:19.221][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.223][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:19.224][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:19.230][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:19.231][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:19.237][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:50:19.238][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:19.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:19.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:19.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:19.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:19.525][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 05:50:19.527][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 05:50:19.529][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 05:50:19.531][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 05:50:19.533][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:50:19.535][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 05:50:19.537][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 05:50:19.539][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 05:50:19.541][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 05:50:19.543][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 05:50:19.545][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:50:19.547][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 05:50:19.549][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 05:50:19.551][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 05:50:19.552][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 05:50:19.554][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 05:50:19.556][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 05:50:19.558][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 05:50:19.560][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:50:19.562][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 05:50:19.564][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 05:50:19.566][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 05:50:19.568][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 05:50:19.569][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 05:50:19.571][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 05:50:19.573][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 05:50:19.575][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 05:50:19.578][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 05:50:19.580][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 05:50:19.582][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 05:50:19.584][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 05:50:19.587][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 05:50:19.589][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 05:50:19.591][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 05:50:19.593][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 05:50:19.595][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 05:50:19.597][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 05:50:19.599][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 05:50:19.601][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 05:50:19.603][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 05:50:19.605][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 05:50:19.607][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 05:50:19.609][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 05:50:19.611][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 05:50:19.613][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 05:50:19.615][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 05:50:19.617][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 05:50:19.620][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 05:50:19.622][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 05:50:19.624][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 05:50:19.626][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 05:50:19.628][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 05:50:19.630][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 05:50:19.632][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 05:50:19.635][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 05:50:19.637][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 05:50:19.639][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 05:50:19.641][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 05:50:19.643][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 05:50:19.645][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 05:50:19.648][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 05:50:19.650][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 05:50:19.652][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 05:50:19.654][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 05:50:20.597][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 05:50:20.612][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 05:50:20.615][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:50:20.617][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:50:20.620][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 05:50:20.622][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 05:50:20.625][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 05:50:20.628][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 05:50:20.630][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 05:50:20.632][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 05:50:20.634][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 05:50:20.637][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 05:50:20.639][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 05:50:20.641][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 05:50:20.644][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 05:50:20.646][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 05:50:20.649][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 05:50:20.651][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 05:50:20.656][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 05:50:20.659][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 05:50:20.705][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:50:20.716][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:50:20.718][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.721][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.760][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[2025-03-07 05:50:20.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.844][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[2025-03-07 05:50:20.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:20.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:20.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:20.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:20.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:20.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:20.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.244][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 05:50:23.267][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 05:50:23.271][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:23.273][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 05:50:23.274][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:23.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:23.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:23.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:23.281][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:23.283][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 05:50:23.285][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 05:50:23.287][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:23.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:23.291][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 05:50:23.293][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 05:50:23.294][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 05:50:23.296][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:23.298][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:23.298][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:23.298][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:23.300][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 05:50:23.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:23.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:23.308][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:23.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:23.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:23.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:23.315][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:50:23.315][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 05:50:23.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:23.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:23.320][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:23.322][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 05:50:23.322][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 05:50:23.325][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:50:23.327][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:50:23.331][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 05:50:23.335][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:50:23.338][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:50:23.341][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:50:23.349][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 05:50:23.351][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 05:50:23.359][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 05:50:23.363][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 05:50:23.365][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:50:23.367][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:50:23.369][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 05:50:23.371][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 05:50:23.373][biodb::testThat]
biodb.INFO [2025-03-07 05:50:23.375][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-07 05:50:23.376][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:50:23.378][biodb::testThat]
biodb.DEBUG[2025-03-07 05:50:23.386][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 05:50:23.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:50:23.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 05:50:23.451][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:50:23.478][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 05:50:23.557][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:50:23.597][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:50:23.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-07 05:50:23.602][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:50:23.610][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2025-03-07 05:50:23.636][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 05:50:23.639][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 05:50:23.640][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 05:50:23.641][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 05:50:23.643][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:23.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:23.647][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:23.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:23.650][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.652][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.INFO [2025-03-07 05:50:23.670][biodb::testContext]
biodb.INFO [2025-03-07 05:50:23.671][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:50:23.673][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-07 05:50:23.674][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 05:50:23.676][biodb::testContext]
biodb.INFO [2025-03-07 05:50:23.680][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:50:23.706][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 05:50:23.719][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:50:23.720][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 05:50:23.722][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.727][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 05:50:23.729][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.733][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[2025-03-07 05:50:23.734][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 05:50:23.736][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.742][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 05:50:23.743][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 05:50:23.745][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 05:50:23.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.751][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 05:50:23.752][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 05:50:23.754][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.759][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 05:50:23.760][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 05:50:23.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.764][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.DEBUG[2025-03-07 05:50:23.766][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 05:50:23.767][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 05:50:23.768][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 05:50:23.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.774][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 05:50:23.775][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.780][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 05:50:23.782][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 05:50:23.783][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 05:50:23.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.789][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:50:23.790][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 05:50:23.791][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 05:50:23.793][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 05:50:23.794][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 05:50:23.796][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 05:50:23.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.800][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[2025-03-07 05:50:23.802][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 05:50:23.803][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 05:50:23.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.816][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 05:50:23.817][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 05:50:23.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.823][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 05:50:23.825][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 05:50:23.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.830][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 05:50:23.832][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 05:50:23.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.838][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 05:50:23.842][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 05:50:23.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:23.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:23.848][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 05:50:23.849][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 05:50:26.843][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 05:50:26.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:26.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:26.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:26.851][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 05:50:26.853][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 05:50:26.855][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 05:50:26.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:26.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:26.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:26.866][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 05:50:26.869][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:26.871][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 05:50:26.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:26.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:26.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.882][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:50:26.884][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:26.886][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.887][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 05:50:26.889][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:26.891][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:26.892][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.894][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:26.894][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:26.894][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:26.894][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:50:26.894][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:50:26.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:26.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:26.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:26.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:26.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:26.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:26.907][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.908][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:26.910][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:26.912][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:26.913][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:26.915][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:26.917][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 05:50:26.921][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:26.923][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:50:26.925][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:26.928][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.930][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:26.934][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:50:26.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:26.940][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.941][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 05:50:26.943][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:26.945][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:26.947][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:26.949][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:26.949][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:26.949][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:26.949][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 05:50:26.949][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 05:50:26.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:26.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:26.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:26.955][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:26.956][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:26.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:26.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:26.998][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:26.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:27.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:27.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.008][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.014][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 05:50:27.021][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.023][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 05:50:27.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:27.032][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.035][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.040][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 05:50:27.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:27.044][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.045][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 05:50:27.047][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:27.048][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.050][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.052][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:27.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:27.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:27.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:27.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:27.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:27.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.063][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.064][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:27.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:27.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.069][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.071][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 05:50:27.074][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.076][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 05:50:27.077][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:27.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.082][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.083][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.087][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 05:50:27.089][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:27.091][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.092][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 05:50:27.094][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:27.096][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.098][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:27.099][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 05:50:27.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:27.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:27.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:27.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:27.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:27.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:27.112][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.114][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:27.115][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:27.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:27.118][self$setPropertyValue]
biodb.DEBUG[2025-03-07 05:50:27.120][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:50:27.122][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.181][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.DEBUG[2025-03-07 05:50:27.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.225][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[2025-03-07 05:50:27.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.233][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[2025-03-07 05:50:27.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.250][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 05:50:27.252][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 05:50:27.254][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 05:50:27.257][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 05:50:27.259][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:50:27.261][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 05:50:27.263][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 05:50:27.266][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 05:50:27.268][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 05:50:27.270][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 05:50:27.273][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:50:27.275][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 05:50:27.277][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 05:50:27.280][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 05:50:27.282][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 05:50:27.284][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 05:50:27.290][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 05:50:27.301][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 05:50:27.304][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:50:27.310][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 05:50:27.317][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 05:50:27.319][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 05:50:27.326][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 05:50:27.328][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 05:50:27.331][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 05:50:27.334][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 05:50:27.336][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 05:50:27.338][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 05:50:27.341][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 05:50:27.343][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 05:50:27.346][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 05:50:27.348][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 05:50:27.351][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 05:50:27.356][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 05:50:27.359][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 05:50:27.361][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 05:50:27.364][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 05:50:27.366][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 05:50:27.369][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 05:50:27.371][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 05:50:27.376][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 05:50:27.378][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 05:50:27.380][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 05:50:27.382][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 05:50:27.384][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 05:50:27.386][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 05:50:27.388][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 05:50:27.391][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 05:50:27.393][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 05:50:27.395][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 05:50:27.397][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 05:50:27.399][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 05:50:27.401][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 05:50:27.403][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 05:50:27.406][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 05:50:27.408][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 05:50:27.410][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 05:50:27.412][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 05:50:27.414][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 05:50:27.416][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 05:50:27.418][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 05:50:27.421][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 05:50:27.423][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 05:50:27.425][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 05:50:27.427][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 05:50:27.429][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 05:50:27.431][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:50:27.433][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:50:27.436][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 05:50:27.438][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 05:50:27.440][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 05:50:27.443][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 05:50:27.445][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 05:50:27.447][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 05:50:27.449][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 05:50:27.451][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 05:50:27.453][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 05:50:27.455][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 05:50:27.457][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 05:50:27.459][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 05:50:27.461][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 05:50:27.463][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 05:50:27.465][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 05:50:27.467][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 05:50:27.477][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 05:50:27.479][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 05:50:27.481][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.483][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.572][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[2025-03-07 05:50:27.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.607][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[2025-03-07 05:50:27.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:27.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:27.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:27.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:27.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:27.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:27.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:27.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:28.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:28.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:28.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:28.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:28.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:28.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:28.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:28.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:28.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:28.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:28.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 05:50:28.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:28.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:28.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:28.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:28.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:28.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 05:50:28.413][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 05:50:28.424][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 05:50:28.427][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:28.429][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 05:50:28.431][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:28.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 05:50:28.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:28.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 05:50:28.443][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:28.453][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 05:50:28.455][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 05:50:28.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 05:50:28.463][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:28.469][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 05:50:28.472][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 05:50:28.478][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 05:50:28.481][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 05:50:28.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 05:50:28.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 05:50:28.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 05:50:28.486][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 05:50:28.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:28.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:28.491][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 05:50:28.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 05:50:28.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 05:50:28.496][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 05:50:28.497][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 05:50:28.497][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 05:50:28.499][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 05:50:28.500][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 05:50:28.502][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 05:50:28.504][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 05:50:28.504][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 05:50:28.506][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 05:50:28.510][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 05:50:28.513][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 05:50:28.516][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 05:50:28.518][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 05:50:28.522][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 05:50:28.529][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 05:50:28.531][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 05:50:28.533][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 05:50:28.537][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 05:50:28.540][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:50:28.541][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 05:50:28.543][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 05:50:28.545][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 05:50:28.548][biodb::testThat]
biodb.INFO [2025-03-07 05:50:28.549][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-07 05:50:28.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 05:50:28.552][biodb::testThat]
biodb.DEBUG[2025-03-07 05:50:28.558][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 05:50:28.667][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:50:28.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 05:50:28.673][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:50:28.694][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 05:50:28.748][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 05:50:28.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 05:50:28.768][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-07 05:50:28.770][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:50:28.797][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-07 05:50:28.838][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-07 05:50:28.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 05:50:28.845][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-07 05:50:28.847][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 05:50:28.853][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2025-03-07 05:50:28.856][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 05:50:28.870][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 05:50:28.872][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 05:50:28.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 05:50:28.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:28.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:28.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:28.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:28.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:28.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 05:50:30.410][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:30.425][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:30.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:30.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:30.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.465][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:50:30.467][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:50:30.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.472][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 05:50:30.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 05:50:30.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.478][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:50:30.480][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:50:30.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 05:50:30.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 05:50:30.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.493][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 05:50:30.495][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 05:50:30.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.500][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 05:50:30.502][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 05:50:30.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.508][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:50:30.510][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:50:30.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:50:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 05:50:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.523][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:50:30.525][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:50:30.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.530][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 05:50:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 05:50:30.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.537][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:50:30.538][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:50:30.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.541][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:50:30.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 05:50:30.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.550][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:50:30.552][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:50:30.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 05:50:30.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 05:50:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.564][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:50:30.566][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:50:30.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 05:50:30.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 05:50:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.577][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:50:30.579][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:50:30.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 05:50:30.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 05:50:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:30.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:30.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 05:50:30.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:30.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:30.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:30.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:30.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:30.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:34.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:36.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:36.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:36.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:36.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:36.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:36.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:36.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:36.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 05:50:36.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 05:50:36.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 05:50:36.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 05:50:36.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 05:50:36.247][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-07 05:50:36.310][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 05:50:36.312][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 05:50:36.318][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 05:50:36.320][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 05:50:36.324][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 05:50:36.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 05:50:36.328][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 05:50:36.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 05:50:36.334][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 05:50:36.335][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 360 ]
>
> proc.time()
user system elapsed
24.763 102.879 387.746
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.081 | 0.091 | 3.604 | |
| ChebiEntry | 0.229 | 0.009 | 0.473 | |