Pierrick Roger
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 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" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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: 2025-04-01 04:18:27 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 04:35:01 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 993.8 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 [2025-04-01 04:33:19.485][biodb::testContext]
biodb.INFO [2025-04-01 04:33:19.487][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:33:19.489][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-04-01 04:33:19.490][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:33:19.492][biodb::testContext]
biodb.INFO [2025-04-01 04:33:19.500][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:33:19.503][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 04:33:19.513][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:33:19.514][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 04:33:19.516][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.522][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 04:33:19.550][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.556][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 04:33:19.558][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.563][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 04:33:19.565][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 04:33:19.567][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 04:33:19.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.571][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[2025-04-01 04:33:19.572][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 04:33:19.574][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 04:33:19.575][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.581][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 04:33:19.582][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 04:33:19.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.588][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 04:33:19.590][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 04:33:19.591][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 04:33:19.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.597][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 04:33:19.599][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.604][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 04:33:19.606][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 04:33:19.607][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 04:33:19.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.613][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:33:19.615][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 04:33:19.616][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 04:33:19.618][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 04:33:19.619][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 04:33:19.621][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 04:33:19.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.626][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 04:33:19.628][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 04:33:19.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.634][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 04:33:19.636][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 04:33:19.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.641][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 04:33:19.643][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 04:33:19.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 04:33:19.650][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 04:33:19.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.656][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 04:33:19.658][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 04:33:19.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.663][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:33:19.665][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 04:33:19.671][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 04:33:19.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.677][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 04:33:19.679][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 04:33:19.681][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 04:33:19.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.690][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 04:33:19.743][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.778][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 04:33:19.780][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:33:19.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.788][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.789][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:33:19.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:33:19.792][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.794][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 04:33:19.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:33:19.796][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.798][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.800][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:33:19.800][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:33:19.800][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:33:19.800][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:33:19.800][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:33:19.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:33:19.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.806][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:33:19.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.810][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.811][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.813][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:33:19.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:33:19.815][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.817][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.818][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 04:33:19.821][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.822][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:33:19.824][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:33:19.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.828][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.829][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.832][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:33:19.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:33:19.835][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.836][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 04:33:19.838][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:33:19.839][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.840][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.842][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:33:19.842][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:33:19.842][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:33:19.842][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:33:19.842][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:33:19.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:33:19.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.847][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:33:19.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.851][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.853][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:33:19.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:33:19.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.858][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.860][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 04:33:19.862][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.864][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 04:33:19.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:33:19.868][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.871][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.872][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.874][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:33:19.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:33:19.877][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.878][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 04:33:19.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:33:19.881][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.882][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.884][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:33:19.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:33:19.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.893][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.894][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.896][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:33:19.897][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:33:19.898][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.899][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.901][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 04:33:19.904][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.905][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:33:19.906][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.908][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:33:19.909][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.910][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.912][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.913][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.914][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:33:19.916][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:33:19.917][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.918][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 04:33:19.920][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:33:19.921][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.922][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:19.924][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.925][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:33:19.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.929][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:33:19.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:19.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:19.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:33:19.934][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:33:19.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:33:19.938][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:19.939][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:33:19.944][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:33:19.945][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:19.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:19.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:19.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:19.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:19.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.051][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 04:33:20.057][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 04:33:20.059][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 04:33:20.061][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 04:33:20.063][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:33:20.064][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 04:33:20.066][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 04:33:20.068][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 04:33:20.070][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 04:33:20.072][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 04:33:20.074][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:33:20.076][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 04:33:20.078][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 04:33:20.080][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 04:33:20.082][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 04:33:20.084][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 04:33:20.086][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 04:33:20.088][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 04:33:20.090][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:33:20.092][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 04:33:20.094][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 04:33:20.095][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 04:33:20.098][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 04:33:20.100][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 04:33:20.102][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 04:33:20.103][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 04:33:20.105][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 04:33:20.107][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 04:33:20.109][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 04:33:20.111][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 04:33:20.113][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 04:33:20.115][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 04:33:20.117][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 04:33:20.118][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 04:33:20.128][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 04:33:20.130][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 04:33:20.131][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 04:33:20.133][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 04:33:20.135][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 04:33:20.137][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 04:33:20.139][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 04:33:20.141][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 04:33:20.142][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 04:33:20.144][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 04:33:20.146][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 04:33:20.148][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 04:33:20.150][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 04:33:20.152][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 04:33:20.153][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 04:33:20.155][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 04:33:20.157][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 04:33:20.159][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 04:33:20.161][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 04:33:20.163][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 04:33:20.165][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 04:33:20.167][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 04:33:20.170][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 04:33:20.172][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 04:33:20.173][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 04:33:20.175][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 04:33:20.177][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 04:33:20.179][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 04:33:20.181][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 04:33:20.183][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 04:33:20.185][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 04:33:20.187][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 04:33:20.189][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:33:20.191][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:33:20.193][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 04:33:20.195][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 04:33:20.197][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 04:33:20.199][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 04:33:20.200][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 04:33:20.202][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 04:33:20.204][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 04:33:20.206][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 04:33:20.208][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 04:33:20.210][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 04:33:20.212][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 04:33:20.214][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 04:33:20.216][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 04:33:20.217][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 04:33:20.219][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 04:33:20.227][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 04:33:20.229][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:33:20.233][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:33:20.235][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.237][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.294][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[2025-04-01 04:33:20.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.321][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[2025-04-01 04:33:20.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:20.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:33:20.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.394][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[2025-04-01 04:33:20.396][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 04:33:20.410][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 04:33:20.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:20.415][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 04:33:20.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:20.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:33:20.420][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:20.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:33:20.423][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:20.424][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 04:33:20.426][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 04:33:20.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:33:20.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:20.431][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 04:33:20.433][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 04:33:20.434][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 04:33:20.436][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 04:33:20.438][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:33:20.438][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:33:20.438][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:33:20.439][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 04:33:20.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:20.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:20.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:33:20.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:33:20.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:33:20.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:33:20.450][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:20.450][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 04:33:20.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:33:20.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:33:20.454][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 04:33:20.456][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 04:33:20.456][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 04:33:20.465][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:33:20.468][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:33:20.470][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 04:33:20.472][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:33:20.475][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:33:20.477][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:33:20.516][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 04:33:20.518][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 04:33:20.523][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 04:33:20.528][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 04:33:20.534][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:33:20.535][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:33:20.537][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 04:33:20.538][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 04:33:20.550][biodb::testThat]
biodb.INFO [2025-04-01 04:33:20.552][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-04-01 04:33:20.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:20.555][biodb::testThat]
biodb.TRACE[2025-04-01 04:33:20.561][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[2025-04-01 04:33:20.563][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:20.568][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:20.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:20.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:20.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:20.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:20.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:20.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:20.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:20.612][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.614][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.617][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.641][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:20.643][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:20.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.646][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.685][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:20.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.691][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:20.693][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:20.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.695][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.703][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:20.704][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:20.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.707][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:20.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.714][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.716][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.719][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.727][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:20.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:20.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.731][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.733][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:20.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:20.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.738][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:20.740][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.743][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.745][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:20.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:20.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:20.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.755][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:20.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:20.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.763][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:20.764][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:20.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.767][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:20.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:20.777][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:20.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.779][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:20.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.787][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:20.789][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:20.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.792][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.793][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:20.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:20.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:20.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:20.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:20.919][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-04-01 04:33:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:20.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:20.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:20.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:20.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:20.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:20.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.005][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:21.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:21.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:21.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.159][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.233][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:21.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.268][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.272][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.305][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.309][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.341][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.343][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.382][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.399][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.410][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.415][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.416][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.419][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.435][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.446][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.452][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.456][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.458][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.473][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.479][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.494][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.495][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.523][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.528][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.534][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.537][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.538][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.573][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.610][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.627][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.631][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.637][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.638][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.641][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.647][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.648][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.651][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.657][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.659][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.661][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.671][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.677][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.679][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.682][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.688][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.689][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.692][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.698][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.702][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.708][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.710][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.713][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.719][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.723][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.733][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 04:33:21.743][biodb::testThat]
biodb.INFO [2025-04-01 04:33:21.745][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-01 04:33:21.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:21.747][biodb::testThat]
biodb.DEBUG[2025-04-01 04:33:21.767][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-04-01 04:33:21.776][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:21.781][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-04-01 04:33:21.783][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:21.785][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-04-01 04:33:21.786][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:21.828][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:21.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:21.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:21.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:21.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:21.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:21.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:21.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:21.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:21.848][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.850][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.852][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:21.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:21.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.884][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.888][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.890][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:21.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.896][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.897][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.900][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:21.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:21.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.907][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.909][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.911][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:21.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:21.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.919][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.920][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.923][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:21.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.933][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.935][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.937][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:21.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.943][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:21.944][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.947][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.949][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:21.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:21.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.957][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.960][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:21.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.967][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.969][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:21.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:21.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.980][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:21.981][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.984][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:21.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:21.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.991][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.993][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:21.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:21.996][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:21.997][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:21.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:22.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:22.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:22.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:22.059][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-04-01 04:33:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-01 04:33:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-01 04:33:22.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-01 04:33:22.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-01 04:33:22.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-01 04:33:22.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-01 04:33:22.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:33:22.086][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.088][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-01 04:33:22.089][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.090][biodb::testThat]
biodb.TRACE[2025-04-01 04:33:22.094][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.096][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.098][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:22.100][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-04-01 04:33:22.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:22.163][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-04-01 04:33:22.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 04:33:22.198][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:22.221][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 04:33:22.223][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:22.225][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 04:33:22.259][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[2025-04-01 04:33:22.263][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:22.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:33:22.267][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:22.269][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 04:33:22.272][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-04-01 04:33:22.289][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:22.291][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:22.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.293][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.295][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.299][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 04:33:22.304][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.306][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-04-01 04:33:22.307][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.308][biodb::testThat]
biodb.TRACE[2025-04-01 04:33:22.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:22.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:22.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:22.454][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[2025-04-01 04:33:22.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:22.461][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:33:22.463][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:22.465][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-04-01 04:33:22.487][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.488][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-04-01 04:33:22.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.491][biodb::testThat]
biodb.TRACE[2025-04-01 04:33:22.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:22.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:22.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:22.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.550][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:22.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:22.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:22.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:22.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:22.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:22.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:22.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:22.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:22.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.632][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-01 04:33:22.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-01 04:33:22.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:22.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:22.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-01 04:33:22.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:22.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:33:22.662][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.663][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-01 04:33:22.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.666][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.676][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.678][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-01 04:33:22.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.680][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.691][biodb::testThat]
biodb.INFO [2025-04-01 04:33:22.693][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-01 04:33:22.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:22.695][biodb::testThat]
biodb.DEBUG[2025-04-01 04:33:22.700][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-04-01 04:33:23.855][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-04-01 04:33:26.928][biodb::testThat]
biodb.INFO [2025-04-01 04:33:26.929][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-01 04:33:26.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:26.932][biodb::testThat]
biodb.DEBUG[2025-04-01 04:33:29.041][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[2025-04-01 04:33:29.893][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:29.895][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:29.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:29.898][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:29.900][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:29.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:29.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:29.904][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 04:33:29.907][biodb::testThat]
biodb.INFO [2025-04-01 04:33:29.908][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-04-01 04:33:29.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:33:29.911][biodb::testThat]
biodb.TRACE[2025-04-01 04:33:29.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:29.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:29.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:29.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:29.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:29.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:29.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:29.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:29.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:29.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:29.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:30.084][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[2025-04-01 04:33:30.089][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:30.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:33:30.094][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:30.096][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 04:33:30.193][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[2025-04-01 04:33:30.198][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:30.199][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:33:30.201][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:30.203][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-04-01 04:33:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 04:33:30.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 04:33:30.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:30.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:30.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:30.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:30.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:30.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:30.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:30.280][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[2025-04-01 04:33:30.286][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:30.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 04:33:30.290][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:30.293][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 04:33:30.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:30.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:30.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:30.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:30.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:30.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:30.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:30.320][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-04-01 04:33:30.389][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:30.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-04-01 04:33:30.393][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:30.395][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:30.396][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:30.398][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:30.399][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:30.400][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:30.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:30.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:30.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:30.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:30.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:30.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:30.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:30.418][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-04-01 04:33:30.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:30.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:30.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-04-01 04:33:31.259][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-04-01 04:33:32.095][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:32.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-04-01 04:33:32.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-04-01 04:33:32.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-04-01 04:33:32.136][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:32.138][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:32.140][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:32.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:32.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:32.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:32.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:32.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:32.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:32.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:32.164][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.169][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.177][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:32.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:32.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.181][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:32.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.189][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:32.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:32.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.203][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:32.204][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:32.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.207][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.215][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:32.217][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:32.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.220][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:32.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.228][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:32.229][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:32.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.251][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.252][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:32.254][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.259][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:32.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.265][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:32.266][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:32.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.269][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:32.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:32.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.278][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:32.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:32.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:32.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:32.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.291][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:32.292][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:32.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.295][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:32.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:32.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.303][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:32.305][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:32.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.307][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:32.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:32.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:32.375][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-04-01 04:33:32.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:32.408][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[2025-04-01 04:33:32.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:32.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 04:33:32.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:32.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 04:33:32.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:32.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:32.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:32.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:32.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:32.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:32.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:32.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:32.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:32.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:32.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:32.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:32.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:32.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:32.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:32.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:32.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:32.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:32.487][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-04-01 04:33:32.489][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:32.491][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-04-01 04:33:32.493][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:32.501][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:32.504][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:32.505][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:32.507][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:32.508][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:32.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:32.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:32.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:32.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:32.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:32.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:32.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:32.543][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-04-01 04:33:32.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:32.568][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:32.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-04-01 04:33:33.416][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-04-01 04:33:34.244][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:34.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-04-01 04:33:34.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-04-01 04:33:34.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-04-01 04:33:34.256][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:34.258][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:34.260][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:34.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:34.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:34.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:34.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:34.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:34.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:34.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:34.278][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.279][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.282][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.289][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:34.291][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:34.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.293][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.295][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:34.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.301][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:34.302][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:34.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.305][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:34.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:34.314][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:34.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.317][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:34.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:34.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.324][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:34.326][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:34.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.328][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:34.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:34.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.336][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:34.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:34.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.340][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.342][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:34.343][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.346][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:34.354][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:34.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.357][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:34.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.364][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:34.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:34.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.368][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:34.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:34.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.376][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:34.377][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:34.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.387][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:34.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:34.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.398][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:34.399][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:34.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.402][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.404][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:34.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:34.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:34.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:34.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:34.466][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-04-01 04:33:34.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:34.507][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[2025-04-01 04:33:34.511][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:33:34.513][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:33:34.515][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:33:34.517][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 04:33:34.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:34.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:34.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:34.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:34.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:34.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:34.534][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[2025-04-01 04:33:34.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:34.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:34.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:34.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:34.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:34.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:34.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:34.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:34.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:34.566][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-04-01 04:33:34.568][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:34.570][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-04-01 04:33:34.572][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:34.573][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:34.575][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:34.576][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:34.578][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:34.579][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:34.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:34.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:34.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:34.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:34.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:34.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:34.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:34.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-04-01 04:33:34.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:34.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:34.604][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-04-01 04:33:35.429][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-04-01 04:33:37.292][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:37.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-04-01 04:33:37.299][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-04-01 04:33:37.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-04-01 04:33:37.304][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:37.306][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:37.307][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:37.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:37.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:37.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:37.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:37.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:37.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:37.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:37.336][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.339][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.346][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:37.348][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:37.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.350][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.352][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:37.353][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:37.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.356][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.358][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:37.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:37.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.362][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.363][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:37.365][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:37.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.367][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.369][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:37.370][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:37.371][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.373][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.374][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:37.376][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.378][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.380][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:37.381][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:37.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.383][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.385][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:37.386][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:37.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.389][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:37.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:37.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.396][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:37.397][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:37.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.400][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.401][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:37.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:37.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.407][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:37.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:37.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.411][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:37.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:37.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:37.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:37.470][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-04-01 04:33:37.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:37.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:37.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:37.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:37.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:37.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:37.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:37.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:37.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:37.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:37.512][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-04-01 04:33:37.514][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:37.516][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-04-01 04:33:37.518][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:37.519][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:37.520][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:37.522][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:37.523][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:37.524][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:37.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:37.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:37.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:37.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:37.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:37.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:37.540][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[2025-04-01 04:33:37.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-04-01 04:33:37.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:37.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:37.549][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-04-01 04:33:40.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-04-01 04:33:40.845][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:40.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-04-01 04:33:40.852][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-04-01 04:33:40.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-04-01 04:33:40.868][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:40.870][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:40.871][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:40.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:40.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:40.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:40.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:40.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:40.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:40.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:40.890][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:40.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:40.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.894][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:40.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:40.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.901][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:40.903][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:40.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.907][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:40.909][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:40.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.911][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.913][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:40.915][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:40.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.917][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.919][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:40.921][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:40.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.925][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:40.927][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:40.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.930][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.931][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:40.933][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:40.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.936][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.937][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:40.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:40.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.944][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:40.945][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:40.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.948][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:40.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:40.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.956][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:40.958][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:40.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.961][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.963][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:40.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:40.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.969][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:40.970][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:40.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.973][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:40.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:40.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:40.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:40.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:40.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:41.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:41.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:41.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:41.033][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-04-01 04:33:41.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:41.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:41.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:41.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:41.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:41.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:41.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:41.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:41.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:41.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:41.079][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-04-01 04:33:41.080][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:41.082][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-04-01 04:33:41.084][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:41.086][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:41.087][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:41.089][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:41.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:41.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:41.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:41.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:41.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:41.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:41.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:41.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:41.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:41.111][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-04-01 04:33:41.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:41.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:41.127][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-04-01 04:33:42.212][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-04-01 04:33:43.047][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:43.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-04-01 04:33:43.054][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-04-01 04:33:43.058][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-04-01 04:33:43.060][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:43.061][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:43.063][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:43.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:43.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:43.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:43.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:43.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:43.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:43.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:43.082][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.086][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.093][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:43.095][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:43.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.097][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.099][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:43.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:43.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.103][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:43.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:43.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.111][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:43.112][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:43.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.115][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:43.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:43.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.120][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.122][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:43.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.126][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.128][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:43.129][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:43.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.132][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.133][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:43.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:43.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.137][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:43.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:43.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.145][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:43.147][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:43.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.156][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:43.158][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:43.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:43.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:43.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:43.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:43.217][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-04-01 04:33:43.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:43.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:43.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:43.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:43.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:43.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:43.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:43.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:43.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:43.260][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-04-01 04:33:43.261][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:43.263][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-04-01 04:33:43.265][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:43.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:43.268][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:43.269][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:43.271][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:43.272][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:43.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:43.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:43.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:43.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:43.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:43.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:43.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:43.301][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-04-01 04:33:43.305][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:43.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:43.309][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-04-01 04:33:44.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-04-01 04:33:45.029][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:45.031][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-04-01 04:33:45.036][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-04-01 04:33:45.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-04-01 04:33:45.041][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:45.042][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:45.044][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:45.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:45.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:45.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:45.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:45.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:45.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:45.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:45.062][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.063][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.065][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.072][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:45.074][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:45.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.076][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.078][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:45.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:45.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.083][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:45.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:45.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.087][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:45.096][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:45.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.098][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:45.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:45.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:45.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.109][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:45.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:45.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:45.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:45.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.120][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.122][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:45.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:45.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.127][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:45.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.131][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:45.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:45.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:45.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:45.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:45.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.149][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:45.150][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:45.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.153][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:45.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:45.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.160][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:45.162][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:45.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.166][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:45.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:45.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:45.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:45.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.175][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:45.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:45.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:45.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:45.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:45.246][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-04-01 04:33:45.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:45.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:45.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:45.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:45.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:45.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:45.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:45.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:45.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:45.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:45.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:45.277][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-04-01 04:33:45.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:45.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-04-01 04:33:45.283][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:45.284][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:45.285][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:45.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:45.288][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:45.289][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:45.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:45.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:45.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:45.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:45.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:45.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:45.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:45.307][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-04-01 04:33:45.311][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:45.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:45.314][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-04-01 04:33:46.140][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-04-01 04:33:46.980][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:46.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-04-01 04:33:46.989][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-04-01 04:33:46.993][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-04-01 04:33:46.995][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:46.997][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:46.999][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:47.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:47.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:47.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:47.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:47.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:47.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:47.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:47.020][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.022][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.024][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.032][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:47.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:47.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.039][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:47.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.045][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:47.046][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:47.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.051][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:47.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:47.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:47.059][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:47.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.062][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:47.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:47.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.070][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:47.072][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:47.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.075][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:47.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.083][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:47.085][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:47.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.088][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.090][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:47.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:47.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.096][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:47.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.103][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:47.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:47.111][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:47.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.114][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:47.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:47.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.123][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:47.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:47.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.128][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:47.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:47.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:47.138][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:47.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.141][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:47.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:47.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.150][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:47.152][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:47.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:47.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:47.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:47.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:47.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:47.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:47.248][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-04-01 04:33:47.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:47.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:47.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:47.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:47.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:47.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:47.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:47.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:47.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:47.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:47.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:47.281][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-04-01 04:33:47.283][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:47.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-04-01 04:33:47.287][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:47.288][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:47.290][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:47.291][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:47.292][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:47.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:47.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:47.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:47.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:47.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:47.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:47.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:47.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:47.311][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-04-01 04:33:47.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:47.317][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:47.319][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-04-01 04:33:48.144][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-04-01 04:33:48.985][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:48.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-04-01 04:33:48.992][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-04-01 04:33:48.995][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-04-01 04:33:48.997][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:48.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:49.000][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:49.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:49.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:49.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:49.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:49.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:49.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:49.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:49.018][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.020][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.029][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:49.031][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:49.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.033][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.041][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:49.042][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:49.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.045][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.046][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:49.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:49.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:49.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:49.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.056][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:49.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:49.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.063][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:49.064][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:49.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.067][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:49.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:49.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.074][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:49.075][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:49.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.078][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.079][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:49.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.083][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.085][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:49.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:49.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:49.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.106][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:49.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:49.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:49.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:49.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.117][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:49.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:49.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:49.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:49.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.129][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.131][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:49.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:49.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:49.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:49.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.141][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:49.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:49.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:49.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:49.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:49.205][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-04-01 04:33:49.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:49.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:49.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:49.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:49.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:49.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:49.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:49.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:49.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:49.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:49.236][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-04-01 04:33:49.238][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:49.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-04-01 04:33:49.241][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:49.243][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:49.244][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:49.246][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:49.247][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:49.248][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:49.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:49.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:49.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:49.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:49.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:49.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:49.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:49.267][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-04-01 04:33:49.270][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:49.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:49.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-04-01 04:33:50.101][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-04-01 04:33:50.941][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:50.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-04-01 04:33:50.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-04-01 04:33:50.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-04-01 04:33:50.954][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:50.956][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:50.957][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:50.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:50.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:50.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:50.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:50.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:50.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:50.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:50.975][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:50.977][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:50.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:50.980][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:50.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:50.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:50.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:50.987][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:50.988][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:50.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:50.991][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:50.993][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:50.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:50.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:50.998][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:51.000][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:51.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:51.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:51.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.021][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:51.022][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:51.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.025][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:51.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:51.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.032][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:51.034][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:51.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.036][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:51.045][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:51.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.050][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:51.051][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:51.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:51.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:51.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.066][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:51.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:51.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.073][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:51.075][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:51.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.077][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:51.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:51.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.085][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:51.086][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:51.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.089][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.097][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:51.098][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:51.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.101][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:51.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:51.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:51.166][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-04-01 04:33:51.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:51.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:51.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:51.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:51.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:51.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:51.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:51.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:51.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:51.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:51.198][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-04-01 04:33:51.200][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:51.202][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-04-01 04:33:51.204][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:51.205][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:51.207][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:51.208][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:51.209][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:51.211][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:51.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:51.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:51.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:51.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:51.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:51.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:51.227][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[2025-04-01 04:33:51.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-04-01 04:33:51.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:51.234][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:51.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-04-01 04:33:52.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-04-01 04:33:52.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:52.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-04-01 04:33:52.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-04-01 04:33:52.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-04-01 04:33:52.895][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:52.897][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:52.898][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:52.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:52.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:52.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:52.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:52.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:52.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:52.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:52.928][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:52.929][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:52.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.932][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:52.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:52.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.939][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:52.941][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:52.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.945][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:52.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.951][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:52.952][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:52.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.955][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:52.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:52.964][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:52.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.966][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:52.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:52.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.974][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:52.975][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:52.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.978][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:52.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:52.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:52.987][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:52.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.990][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.991][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:52.993][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:52.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:52.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.003][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:53.004][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:53.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.007][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:53.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.014][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:53.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:53.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:53.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:53.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.026][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:53.027][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:53.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.030][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.032][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:53.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:53.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.037][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:53.039][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:53.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.042][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:53.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:53.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:53.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:53.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:53.104][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-04-01 04:33:53.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:53.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:53.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:53.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:53.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:53.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:53.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:53.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:53.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:53.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:53.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:53.136][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-04-01 04:33:53.137][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:53.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-04-01 04:33:53.141][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:53.143][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:53.144][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:53.146][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:53.155][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:53.156][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:53.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:53.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:53.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:53.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:53.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:53.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:53.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:53.175][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-04-01 04:33:53.179][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:53.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:53.182][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-04-01 04:33:54.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-04-01 04:33:54.844][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:54.846][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-04-01 04:33:54.851][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-04-01 04:33:54.855][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-04-01 04:33:54.857][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:54.858][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:54.860][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:54.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:54.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:54.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:54.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:54.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:54.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:54.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:54.878][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:54.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:54.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.882][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:54.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:54.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.889][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:54.891][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:54.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.894][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.895][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:54.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:54.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.901][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:54.903][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:54.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:54.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:54.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.913][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:54.914][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:54.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.917][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:54.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:54.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.924][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:54.926][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:54.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.928][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:54.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.936][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:54.937][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:54.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.940][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.941][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:54.943][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:54.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.945][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.947][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:54.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:54.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:54.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:54.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.957][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:54.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:54.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.965][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:54.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:54.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:54.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.976][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:54.978][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:54.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.981][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:54.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.988][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:54.989][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:54.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.992][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:54.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:54.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:55.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:55.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:55.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:55.099][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-04-01 04:33:55.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:55.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:55.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:55.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:55.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:55.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:55.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:55.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:55.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:55.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:55.131][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-04-01 04:33:55.133][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:55.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-04-01 04:33:55.137][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:55.138][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:55.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:55.141][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:55.142][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:55.144][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:55.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:55.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:55.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:55.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:55.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:55.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:55.160][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[2025-04-01 04:33:55.162][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-04-01 04:33:55.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:55.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:55.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-04-01 04:33:56.018][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-04-01 04:33:56.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:56.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-04-01 04:33:56.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-04-01 04:33:56.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-04-01 04:33:56.872][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:56.874][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:56.876][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:56.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:56.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:56.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:56.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:56.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:56.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:56.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:56.900][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:56.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:56.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:56.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:56.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.913][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:56.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:56.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.917][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.919][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:56.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.925][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:56.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:56.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.930][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:56.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:56.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.938][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:56.939][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:56.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.942][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:56.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:56.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.950][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:56.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:56.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.954][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.962][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:56.964][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:56.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.967][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.969][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:56.970][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:56.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.973][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.975][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:56.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:56.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.981][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:56.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:56.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.986][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:56.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:56.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:56.994][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:56.995][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:56.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:56.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:57.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:57.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.005][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:57.007][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:57.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.010][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.011][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:57.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.017][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:57.019][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:57.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:57.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:57.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:57.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:57.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:57.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:57.110][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-04-01 04:33:57.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:57.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:57.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:57.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:57.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:57.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:57.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:57.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:57.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:57.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:57.146][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-04-01 04:33:57.147][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:57.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-04-01 04:33:57.152][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:57.153][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:57.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:57.156][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:57.158][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:57.159][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:57.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:57.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:57.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:57.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:57.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:57.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:57.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:57.178][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-04-01 04:33:57.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:57.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:57.186][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-04-01 04:33:58.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-04-01 04:33:58.931][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:33:58.935][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-04-01 04:33:58.939][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-04-01 04:33:58.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-04-01 04:33:58.945][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:33:58.947][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:33:58.949][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:33:58.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:58.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:58.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:58.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:58.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:58.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:58.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:33:58.968][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:58.970][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:58.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:58.972][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:58.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:58.980][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:58.982][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:58.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:58.985][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:58.986][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:33:58.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:33:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:58.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:58.993][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:58.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:58.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:58.997][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:33:59.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:33:59.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:33:59.007][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:33:59.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.010][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:33:59.013][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:33:59.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.016][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.017][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:59.019][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:33:59.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.023][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:59.024][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.027][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.029][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:33:59.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.034][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:59.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:59.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.038][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:33:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.045][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:59.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:59.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.049][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:33:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:33:59.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:59.071][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:59.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.074][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:33:59.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:33:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.081][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:33:59.083][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:33:59.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.085][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:33:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:33:59.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:33:59.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:59.144][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-04-01 04:33:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:33:59.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:33:59.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:33:59.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:33:59.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:59.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:59.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:59.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:59.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:59.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:59.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:33:59.178][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-04-01 04:33:59.180][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:33:59.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-04-01 04:33:59.184][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:33:59.186][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:33:59.187][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:33:59.189][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:33:59.190][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:33:59.192][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:33:59.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:33:59.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:33:59.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:33:59.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:33:59.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:33:59.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:33:59.209][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[2025-04-01 04:33:59.211][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-04-01 04:33:59.215][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:33:59.216][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:33:59.218][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-04-01 04:34:00.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-04-01 04:34:01.363][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:01.366][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-04-01 04:34:01.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-04-01 04:34:01.374][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-04-01 04:34:01.376][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:01.378][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:01.380][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:01.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:01.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:01.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:01.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:01.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:01.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:01.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:01.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.401][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.404][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.412][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.414][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.417][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.419][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.425][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.429][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:01.439][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:01.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.442][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.444][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.448][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.450][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.452][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.455][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.456][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.458][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.461][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.471][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.489][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.497][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:01.499][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:01.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.502][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:01.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:01.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.510][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:01.511][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:01.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.514][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.516][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:01.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:01.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:01.524][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:01.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.527][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:01.586][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-04-01 04:34:01.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:01.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:01.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:01.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:01.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:01.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:01.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:01.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:01.618][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-04-01 04:34:01.619][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:01.622][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-04-01 04:34:01.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:01.626][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2025-04-01 04:34:01.628][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:01.629][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:01.631][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:01.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:01.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:01.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:01.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:01.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:01.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:01.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:01.649][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.653][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.661][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.662][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.665][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.666][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.672][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.676][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.678][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:01.685][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:01.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.688][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:01.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:01.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.695][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.697][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.699][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.707][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.711][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.713][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.714][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.717][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.718][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.731][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.733][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.736][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.744][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:01.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:01.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.748][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:01.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.755][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:01.757][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:01.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.759][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.761][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:01.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.767][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:01.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:01.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.771][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.773][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:01.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:01.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:01.834][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-04-01 04:34:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:01.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:01.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:01.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:01.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:01.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:01.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:01.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:01.867][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-04-01 04:34:01.869][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:01.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-04-01 04:34:01.873][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:01.875][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2025-04-01 04:34:01.877][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:01.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:01.880][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:01.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:01.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:01.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:01.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:01.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:01.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:01.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:01.899][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.903][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:01.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:01.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.911][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.912][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.915][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:01.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:01.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.923][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.924][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.927][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:01.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.934][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:01.936][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:01.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.939][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:01.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:01.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.950][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:01.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.958][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.959][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:01.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.962][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.964][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.968][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.970][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.976][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.986][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.988][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:01.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:01.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:01.996][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:01.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:01.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.000][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.012][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.019][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.021][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.023][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.087][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-04-01 04:34:02.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:02.119][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-04-01 04:34:02.121][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:02.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-04-01 04:34:02.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:02.127][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2025-04-01 04:34:02.129][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:02.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:02.132][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:02.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:02.150][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.152][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.154][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.162][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.163][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.166][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.173][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.175][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.177][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.196][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.198][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.200][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.208][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.209][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.212][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.214][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.219][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.225][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.237][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.245][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.249][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.258][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.260][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.267][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.269][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.272][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.335][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-04-01 04:34:02.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.365][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[2025-04-01 04:34:02.367][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-04-01 04:34:02.368][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:02.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-04-01 04:34:02.372][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:02.374][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2025-04-01 04:34:02.376][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:02.378][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:02.379][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:02.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:02.397][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.402][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.409][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.411][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.413][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.421][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.425][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.427][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.439][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.447][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.448][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.458][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.460][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.463][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.464][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.466][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.468][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.486][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.488][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.496][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.497][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.500][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.508][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.509][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.512][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.514][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.519][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.521][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.524][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.525][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.586][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-04-01 04:34:02.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:02.618][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-04-01 04:34:02.619][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:02.622][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-04-01 04:34:02.623][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:02.626][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2025-04-01 04:34:02.627][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:02.629][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:02.631][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:02.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:02.649][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.653][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.661][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.662][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.665][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.673][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.677][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.685][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.690][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.697][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.699][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.702][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.709][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.711][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.713][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.715][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.717][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.719][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.735][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.736][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.739][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.746][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.748][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.750][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:02.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:02.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.758][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.759][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.764][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:02.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.769][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.773][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:02.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:02.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:02.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.839][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-04-01 04:34:02.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:02.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.871][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[2025-04-01 04:34:02.872][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-04-01 04:34:02.874][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:02.876][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-04-01 04:34:02.878][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:02.880][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2025-04-01 04:34:02.882][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:02.884][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:02.886][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:02.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:02.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:02.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:02.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:02.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:02.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:02.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:02.905][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.906][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.909][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:02.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:02.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.916][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.918][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.921][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.922][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:02.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:02.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.928][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.933][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:02.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:02.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.945][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:02.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:02.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.953][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.958][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:02.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.966][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.967][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:02.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.970][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.972][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.976][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:02.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:02.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.993][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:02.996][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:02.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:03.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.003][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:03.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:03.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.007][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:03.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:03.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.015][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:03.016][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:03.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.019][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.021][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:03.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.026][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:03.028][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:03.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.030][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:03.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:03.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.093][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-04-01 04:34:03.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.123][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[2025-04-01 04:34:03.125][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-04-01 04:34:03.126][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:03.128][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-04-01 04:34:03.130][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:03.133][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2025-04-01 04:34:03.134][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:03.136][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:03.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:03.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.155][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.157][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.160][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.167][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:03.168][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:03.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.171][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:03.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:03.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.178][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:03.180][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:03.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.185][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:03.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:03.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.190][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:03.192][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:03.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:03.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:03.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.202][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:03.203][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:03.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.206][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:03.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:03.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.214][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:03.215][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:03.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.220][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:03.221][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.240][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:03.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:03.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:03.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:03.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.252][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:03.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:03.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.257][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:03.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.264][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:03.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:03.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.269][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.270][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:03.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:03.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:03.278][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:03.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.280][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:03.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:03.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:03.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:03.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:03.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.345][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-04-01 04:34:03.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.387][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[2025-04-01 04:34:03.392][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:03.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:34:03.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:03.397][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 04:34:03.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.444][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[2025-04-01 04:34:03.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.582][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[2025-04-01 04:34:03.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.647][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[2025-04-01 04:34:03.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.680][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.TRACE[2025-04-01 04:34:03.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.947][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.TRACE[2025-04-01 04:34:03.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:03.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:03.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:03.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:03.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:03.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:03.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:03.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:03.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:03.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:03.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:03.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:04.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:04.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:04.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:04.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:04.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:04.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:04.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:04.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:04.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:04.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:04.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:04.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:04.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:04.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:04.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:04.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:04.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:04.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:04.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:04.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:04.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:04.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:04.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:04.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:04.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:04.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:04.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:04.179][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-04-01 04:34:04.183][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-04-01 04:34:04.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:04.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:04.189][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:05.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:05.891][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:05.894][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-04-01 04:34:05.899][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-04-01 04:34:05.903][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[2025-04-01 04:34:05.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:05.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:05.912][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:08.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:08.872][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-04-01 04:34:08.875][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-04-01 04:34:08.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-04-01 04:34:08.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-04-01 04:34:08.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:08.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:08.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:08.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:08.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:08.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:08.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:08.916][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-04-01 04:34:08.917][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:08.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-04-01 04:34:08.921][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:34:08.923][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:34:08.924][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:08.926][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:08.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:34:08.929][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:34:08.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:08.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:08.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:08.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:08.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:08.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:08.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:08.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-04-01 04:34:08.951][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:08.952][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:08.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-04-01 04:34:09.780][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-04-01 04:34:10.634][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:10.636][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-04-01 04:34:10.641][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-04-01 04:34:10.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-04-01 04:34:10.646][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:10.648][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:10.649][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:10.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:10.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:10.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:10.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:10.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:10.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:10.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:10.667][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.671][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.679][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:10.680][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:10.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.683][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.684][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:10.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:10.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.690][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:10.691][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:10.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.694][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:10.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:10.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.701][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:10.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:10.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.705][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:10.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:10.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.713][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:10.714][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:10.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.717][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:10.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:10.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:10.725][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:10.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.728][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.730][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:10.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:10.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.735][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:10.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:10.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.739][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.741][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:10.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:10.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.748][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.750][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.758][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:10.759][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:10.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:10.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:10.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.769][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:10.771][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:10.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.773][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.775][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:10.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:10.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.781][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:10.782][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:10.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.785][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:10.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:10.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:10.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:10.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:10.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:10.859][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-04-01 04:34:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:10.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:10.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:10.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:10.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:10.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:10.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:10.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:10.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:10.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:10.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:10.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:10.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:10.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:10.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:10.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:10.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:10.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:10.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:10.921][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-04-01 04:34:10.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:10.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-04-01 04:34:10.926][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:34:10.927][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:34:10.929][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:10.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:10.932][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:34:10.938][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:34:10.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:10.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:10.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:10.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:10.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:10.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:10.959][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[2025-04-01 04:34:10.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-04-01 04:34:10.966][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:10.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:10.970][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-04-01 04:34:11.799][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-04-01 04:34:12.641][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:12.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-04-01 04:34:12.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-04-01 04:34:12.653][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-04-01 04:34:12.656][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:12.658][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:12.659][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:12.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:12.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:12.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:12.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:12.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:12.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:12.680][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.684][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.692][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:12.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:12.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.697][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.699][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:12.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.705][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:12.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:12.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.709][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:12.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:12.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.717][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:12.719][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:12.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.722][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:12.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:12.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.730][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:12.731][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:12.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.734][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:12.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.762][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:12.764][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:12.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.767][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.769][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:12.771][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:12.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.774][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.776][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:12.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:12.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.784][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.787][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.797][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:12.798][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:12.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.802][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:12.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.811][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:12.813][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:12.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.816][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:12.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:12.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:12.826][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:12.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.829][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:12.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:12.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:12.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:12.902][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-04-01 04:34:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:12.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:12.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:12.947][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[2025-04-01 04:34:12.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:12.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:12.956][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:13.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:14.879][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:14.882][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-04-01 04:34:14.887][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-04-01 04:34:14.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:14.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:14.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:14.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:14.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:14.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:14.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:14.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:14.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:14.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:14.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:14.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:14.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:14.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:14.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:14.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:14.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:14.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:14.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:14.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:14.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:14.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:14.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:14.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:14.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.608][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:15.613][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:15.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-04-01 04:34:15.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:15.618][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-04-01 04:34:15.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:15.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:15.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:15.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:15.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:15.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:15.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:15.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:15.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:15.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:15.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:16.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:16.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:16.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:34:16.390][biodb::testThat]
biodb.INFO [2025-04-01 04:34:16.391][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-04-01 04:34:16.393][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:16.394][biodb::testThat]
biodb.TRACE[2025-04-01 04:34:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 04:34:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 04:34:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:16.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:16.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:16.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:16.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:16.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:16.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:16.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:16.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:16.457][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:16.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:16.461][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:17.290][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:18.114][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:18.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-04-01 04:34:18.122][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-04-01 04:34:18.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:18.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:18.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:18.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:18.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:18.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:18.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:18.170][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[2025-04-01 04:34:18.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:18.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:18.178][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:19.005][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:19.830][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:19.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-04-01 04:34:19.837][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-04-01 04:34:19.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:19.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:19.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:19.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:19.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:19.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:19.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:19.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:19.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:19.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:19.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:19.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:19.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:19.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:19.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:19.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:19.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:19.902][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:19.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:19.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:19.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:19.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:19.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:19.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:19.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:19.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.929][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:19.930][private$selectFields]
biodb.TRACE[2025-04-01 04:34:19.931][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:19.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:19.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:19.935][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.937][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.939][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.945][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.946][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:19.947][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:19.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.953][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.954][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:19.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:19.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:19.985][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 04:34:19.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:19.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:19.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:19.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:19.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:19.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:19.999][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.TRACE[2025-04-01 04:34:20.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.012][private$selectFields]
biodb.TRACE[2025-04-01 04:34:20.014][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:20.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:20.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.023][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.035][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.038][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.041][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.047][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.048][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:20.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:20.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:20.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:20.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:20.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:20.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:20.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:20.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:20.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.096][private$selectFields]
biodb.TRACE[2025-04-01 04:34:20.097][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:20.099][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:20.100][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.105][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.107][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.108][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.111][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.114][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:20.115][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.116][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.119][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.120][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.139][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 04:34:20.140][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:20.142][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:20.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:20.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:20.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:20.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:20.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:20.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:20.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:20.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:20.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:20.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:20.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:20.276][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:20.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:20.282][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:20.285][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:21.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:22.954][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:22.957][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-04-01 04:34:22.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-04-01 04:34:22.966][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[2025-04-01 04:34:22.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:22.972][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:22.974][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:23.805][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:24.630][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:24.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-04-01 04:34:24.638][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-04-01 04:34:24.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:24.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:24.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:24.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:24.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:24.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:24.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:24.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:24.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:24.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:24.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:24.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:24.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:24.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:24.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:24.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:24.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:24.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:24.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:24.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:24.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:24.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:24.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:24.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:24.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:24.771][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:24.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:24.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:24.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:24.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:24.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:24.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:24.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:24.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.849][private$selectFields]
biodb.TRACE[2025-04-01 04:34:24.850][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:24.852][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:24.853][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.858][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.860][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.862][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.865][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.866][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.867][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.869][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.870][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.873][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.874][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.892][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 04:34:24.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:24.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:24.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:24.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:24.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:24.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:24.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.966][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.968][private$selectFields]
biodb.TRACE[2025-04-01 04:34:24.969][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:24.970][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:24.972][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.973][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.977][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:24.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:24.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:24.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:24.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.002][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.004][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.006][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.024][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:25.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.059][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.060][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.061][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.063][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.064][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.065][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.067][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.069][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.071][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.072][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.075][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.076][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.078][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.083][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.084][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.102][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 04:34:25.104][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:25.105][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:25.116][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:25.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:25.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:34:25.126][biodb::testThat]
biodb.INFO [2025-04-01 04:34:25.127][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-04-01 04:34:25.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:25.129][biodb::testThat]
biodb.TRACE[2025-04-01 04:34:25.133][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 04:34:25.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 04:34:25.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:25.180][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:25.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:25.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 04:34:25.188][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:25.190][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 04:34:25.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.226][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:25.230][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:25.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 04:34:25.233][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:25.235][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 04:34:25.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.310][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:25.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.339][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.340][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.341][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.346][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.348][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.351][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.354][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.356][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.358][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.359][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.362][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.363][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.381][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 04:34:25.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.407][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.408][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.409][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.411][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.412][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.413][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.417][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.420][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.422][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.424][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.425][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.428][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.429][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.430][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.432][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.450][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:25.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.477][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.478][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.480][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.481][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.482][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.484][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.486][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.489][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.492][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.493][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.494][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.499][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.501][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.527][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 04:34:25.528][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:25.530][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:25.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:25.586][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:25.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-01 04:34:25.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:25.591][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-01 04:34:25.596][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:25.600][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:25.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-01 04:34:25.603][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:25.605][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-01 04:34:25.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:25.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.701][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:25.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.727][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.728][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.729][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.731][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.732][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.733][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.735][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.737][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.740][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.743][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.751][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.754][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.760][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.761][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.779][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 04:34:25.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.805][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.807][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.808][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.810][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.812][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.813][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.816][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.819][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.821][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.824][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.830][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.831][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.849][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:25.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:25.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:25.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:25.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:25.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:25.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.876][private$selectFields]
biodb.TRACE[2025-04-01 04:34:25.878][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:25.879][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:25.880][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.882][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.883][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.886][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.887][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.888][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.891][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.892][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.893][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:25.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.899][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.900][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:25.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.918][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 04:34:25.919][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:25.921][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:25.932][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:25.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:25.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:34:25.941][biodb::testThat]
biodb.INFO [2025-04-01 04:34:25.943][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-04-01 04:34:25.944][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:25.945][biodb::testThat]
biodb.TRACE[2025-04-01 04:34:25.949][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-01 04:34:25.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-01 04:34:25.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:25.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:25.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:25.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:25.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:25.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:25.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:26.007][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:26.012][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:26.013][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-04-01 04:34:26.015][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:26.017][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-04-01 04:34:26.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.052][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:26.056][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:26.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-04-01 04:34:26.059][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:26.061][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-04-01 04:34:26.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:26.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.125][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:26.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.153][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.155][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.156][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.157][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.160][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.163][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.164][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.168][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.171][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.172][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.174][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.176][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.178][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.196][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-04-01 04:34:26.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.210][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[2025-04-01 04:34:26.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.232][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.234][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.235][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.242][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.243][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.245][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.248][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.249][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.250][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.256][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.257][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.275][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:26.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.302][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.303][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.304][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.306][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.307][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.308][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.310][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.313][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.315][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.318][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.319][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.321][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.322][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.323][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.326][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.327][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.345][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-04-01 04:34:26.347][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:26.348][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:26.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:26.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:26.420][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:26.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-04-01 04:34:26.424][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:26.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-04-01 04:34:26.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:26.434][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:26.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-04-01 04:34:26.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:26.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-04-01 04:34:26.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:26.543][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-04-01 04:34:26.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.572][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.575][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.582][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.587][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.588][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.590][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.595][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.597][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.615][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-04-01 04:34:26.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.642][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.644][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.645][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.646][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.647][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.653][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.659][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.660][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.661][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.666][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.668][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.686][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-04-01 04:34:26.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:26.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.721][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.723][private$selectFields]
biodb.TRACE[2025-04-01 04:34:26.724][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-04-01 04:34:26.725][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-04-01 04:34:26.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.732][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.733][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.735][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.737][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.739][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.740][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-04-01 04:34:26.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.745][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.747][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-04-01 04:34:26.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:26.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:26.765][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-04-01 04:34:26.766][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-04-01 04:34:26.767][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-04-01 04:34:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:26.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-04-01 04:34:26.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-01 04:34:26.802][biodb::testThat]
biodb.INFO [2025-04-01 04:34:26.803][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-04-01 04:34:26.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:26.805][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:26.808][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-04-01 04:34:26.809][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:26.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-04-01 04:34:26.813][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:34:26.815][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:34:26.816][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:26.818][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:26.819][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:34:26.820][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:34:26.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:26.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:26.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:26.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:26.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:26.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:26.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:26.838][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-04-01 04:34:26.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:26.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:26.845][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-04-01 04:34:27.669][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-04-01 04:34:28.495][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:28.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-04-01 04:34:28.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-04-01 04:34:28.506][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-04-01 04:34:28.508][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:28.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:28.511][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:28.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:28.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:28.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:28.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:28.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:28.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:28.526][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[2025-04-01 04:34:28.529][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.533][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.540][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:28.542][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:28.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.544][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.546][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:28.547][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:28.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.550][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.552][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:28.553][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:28.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.556][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.558][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:28.559][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:28.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.562][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.563][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:28.565][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:28.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.567][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.569][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:28.570][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:28.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.573][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:28.576][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:28.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.578][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.580][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:28.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:28.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.596][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.598][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:28.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:28.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.603][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.604][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:28.606][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:28.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.608][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:28.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:28.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:28.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:28.668][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-04-01 04:34:28.670][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-04-01 04:34:28.680][biodb::testThat]
biodb.INFO [2025-04-01 04:34:28.681][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-04-01 04:34:28.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:28.684][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:28.697][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-04-01 04:34:28.698][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-04-01 04:34:28.700][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-04-01 04:34:28.702][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-04-01 04:34:28.704][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-04-01 04:34:28.705][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:34:28.707][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:28.708][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:28.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:34:28.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:34:28.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:28.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:28.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:28.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:28.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:28.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:28.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:28.731][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-04-01 04:34:28.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:28.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:28.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-04-01 04:34:29.563][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-04-01 04:34:30.391][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:30.394][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-04-01 04:34:30.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-04-01 04:34:30.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:30.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:30.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:30.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:30.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:30.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:30.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:30.414][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-04-01 04:34:30.418][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:30.419][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:30.421][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-04-01 04:34:31.250][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-04-01 04:34:32.077][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:32.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-04-01 04:34:32.084][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-04-01 04:34:32.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:32.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:32.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:32.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:32.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:32.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:32.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:32.101][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-04-01 04:34:32.104][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:32.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:32.108][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-04-01 04:34:32.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-04-01 04:34:33.777][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:33.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-04-01 04:34:33.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-04-01 04:34:33.788][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-04-01 04:34:33.790][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:33.792][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-04-01 04:34:33.793][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:33.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:33.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:33.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:33.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:33.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:33.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:33.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:33.831][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.833][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.835][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.843][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:33.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:33.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.847][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.849][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:33.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:33.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.853][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.855][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:33.856][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:33.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.859][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:33.862][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:33.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.864][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:33.868][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:33.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.870][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.872][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:33.873][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:33.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.876][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.878][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:33.879][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:33.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.882][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:33.885][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:33.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.887][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.889][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:33.891][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:33.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.894][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.895][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:33.897][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:33.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.899][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:33.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:33.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:33.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:33.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:33.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:33.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:33.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:33.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:33.956][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.957][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.960][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:33.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:33.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.967][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:33.969][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:33.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.971][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.973][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:33.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:33.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.978][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:33.980][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:33.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:33.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:33.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.990][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:33.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:33.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:33.994][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:33.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:33.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:33.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.006][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.013][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.017][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.025][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:34.026][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:34.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.029][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.030][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:34.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:34.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.036][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.037][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.040][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.057][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:34.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:34.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:34.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:34.070][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:34.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.073][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.074][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:34.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:34.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.080][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:34.082][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:34.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.084][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.086][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:34.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:34.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:34.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:34.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:34.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:34.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:34.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:34.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:34.146][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.157][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:34.158][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:34.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.161][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:34.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:34.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.168][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:34.170][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:34.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.172][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:34.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:34.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.179][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:34.181][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:34.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:34.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:34.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.195][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:34.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.206][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.208][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:34.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.214][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:34.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:34.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.218][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.219][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:34.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:34.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.225][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.227][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:34.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.237][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:34.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:34.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.241][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:34.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:34.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.249][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:34.250][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:34.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.253][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:34.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:34.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.260][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:34.262][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:34.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.264][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:34.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:34.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:34.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:34.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:34.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:34.370][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-04-01 04:34:34.371][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-04-01 04:34:34.372][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-04-01 04:34:34.388][biodb::testThat]
biodb.INFO [2025-04-01 04:34:34.390][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-04-01 04:34:34.391][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:34.392][biodb::testThat]
biodb.INFO [2025-04-01 04:34:34.424][biodb::testThat]
biodb.INFO [2025-04-01 04:34:34.425][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-04-01 04:34:34.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:34.428][biodb::testThat]
biodb.INFO [2025-04-01 04:34:34.438][biodb::testThat]
biodb.INFO [2025-04-01 04:34:34.440][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-04-01 04:34:34.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:34.442][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:34.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:34.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:34.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:34.454][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:35.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:36.292][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:36.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-04-01 04:34:36.300][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-04-01 04:34:36.316][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:36.318][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:36.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:36.320][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:36.322][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:36.323][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:36.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:36.326][ef$get] fields variable is a list.
biodb.INFO [2025-04-01 04:34:36.328][biodb::testThat]
biodb.INFO [2025-04-01 04:34:36.329][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-04-01 04:34:36.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:36.331][biodb::testThat]
biodb.ERROR[2025-04-01 04:34:36.358][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-04-01 04:34:36.386][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-04-01 04:34:36.405][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 04:34:36.406][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 04:34:36.408][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 04:34:36.409][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 04:34:36.410][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:36.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:36.413][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.415][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 04:34:36.430][biodb::testContext]
biodb.INFO [2025-04-01 04:34:36.431][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:36.432][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-04-01 04:34:36.434][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:36.435][biodb::testContext]
biodb.INFO [2025-04-01 04:34:36.438][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:36.440][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:36.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:36.446][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 04:34:36.447][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.453][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 04:34:36.455][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.460][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 04:34:36.462][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.467][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 04:34:36.469][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 04:34:36.470][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 04:34:36.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.474][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[2025-04-01 04:34:36.476][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 04:34:36.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 04:34:36.479][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.484][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 04:34:36.486][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 04:34:36.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.490][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.DEBUG[2025-04-01 04:34:36.492][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 04:34:36.493][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 04:34:36.495][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 04:34:36.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.500][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 04:34:36.501][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.505][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[2025-04-01 04:34:36.507][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 04:34:36.508][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 04:34:36.510][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 04:34:36.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.515][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:36.517][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 04:34:36.518][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 04:34:36.520][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 04:34:36.521][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 04:34:36.523][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 04:34:36.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.528][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 04:34:36.530][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 04:34:36.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.536][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 04:34:36.537][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 04:34:36.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.543][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 04:34:36.544][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 04:34:36.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.550][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 04:34:36.551][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 04:34:36.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.557][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 04:34:36.558][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 04:34:36.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.564][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:36.565][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 04:34:36.570][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 04:34:36.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.575][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 04:34:36.577][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 04:34:36.578][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 04:34:36.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.583][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 04:34:36.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 04:34:36.589][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.590][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:36.591][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.593][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.594][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.597][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:36.607][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:36.609][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.611][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 04:34:36.612][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:36.614][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.615][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.616][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:36.616][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:36.616][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:36.616][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:36.616][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:36.618][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:36.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:36.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.626][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.627][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:36.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:36.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.632][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.634][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 04:34:36.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:36.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.641][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:36.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.643][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.647][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:36.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:36.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.652][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 04:34:36.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:36.654][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:36.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:36.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:36.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:36.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:36.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:36.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.663][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:36.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.667][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.668][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:36.671][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:36.672][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.673][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.675][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 04:34:36.678][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.679][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 04:34:36.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.682][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:36.683][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.685][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.686][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.688][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.689][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:36.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:36.692][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.694][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 04:34:36.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:36.697][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.698][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.700][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.701][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:36.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:36.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.711][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:36.714][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:36.716][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.717][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.719][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 04:34:36.722][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.723][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:36.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:36.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.732][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.734][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:36.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:36.737][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.738][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 04:34:36.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:36.741][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.743][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:36.744][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.746][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:36.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:36.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:36.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:36.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:36.756][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:36.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:36.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:36.762][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:36.764][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:36.765][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.787][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[2025-04-01 04:34:36.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.829][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[2025-04-01 04:34:36.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.835][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[2025-04-01 04:34:36.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.872][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[2025-04-01 04:34:36.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:36.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:36.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:36.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:36.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:36.894][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 04:34:36.897][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 04:34:36.899][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 04:34:36.901][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 04:34:36.904][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:36.906][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 04:34:36.909][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:36.911][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:36.913][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 04:34:36.916][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 04:34:36.918][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:36.920][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 04:34:36.923][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:36.925][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:36.927][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 04:34:36.930][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 04:34:36.932][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 04:34:36.934][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 04:34:36.936][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:36.939][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 04:34:36.941][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 04:34:36.943][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 04:34:36.945][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 04:34:36.947][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 04:34:36.949][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 04:34:36.951][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 04:34:36.953][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 04:34:36.955][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 04:34:36.957][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 04:34:36.959][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 04:34:36.961][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 04:34:36.963][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 04:34:36.965][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 04:34:36.967][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 04:34:36.969][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 04:34:36.971][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 04:34:36.973][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 04:34:36.975][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 04:34:36.977][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 04:34:36.979][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 04:34:36.981][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 04:34:36.983][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 04:34:36.985][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 04:34:36.987][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 04:34:36.989][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 04:34:36.991][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 04:34:36.993][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 04:34:36.995][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 04:34:36.997][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 04:34:36.999][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 04:34:37.001][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 04:34:37.003][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 04:34:37.005][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 04:34:37.007][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 04:34:37.009][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 04:34:37.011][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 04:34:37.013][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 04:34:37.015][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 04:34:37.017][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 04:34:37.019][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 04:34:37.021][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 04:34:37.023][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 04:34:37.025][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 04:34:37.027][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 04:34:37.029][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 04:34:37.031][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 04:34:37.033][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:37.035][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:37.037][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 04:34:37.039][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 04:34:37.041][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 04:34:37.043][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 04:34:37.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 04:34:37.047][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 04:34:37.049][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 04:34:37.051][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 04:34:37.053][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 04:34:37.055][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 04:34:37.058][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 04:34:37.060][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 04:34:37.062][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 04:34:37.064][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 04:34:37.066][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 04:34:37.068][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 04:34:37.070][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:37.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:37.073][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.075][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.076][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[2025-04-01 04:34:37.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.285][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[2025-04-01 04:34:37.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.357][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[2025-04-01 04:34:37.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.365][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[2025-04-01 04:34:37.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.380][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[2025-04-01 04:34:37.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:37.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:37.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:37.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:37.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:37.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:37.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:37.398][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:37.400][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 04:34:37.402][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:37.404][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 04:34:37.405][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:37.406][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:37.407][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:37.409][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:37.410][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:37.411][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 04:34:37.413][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 04:34:37.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:37.415][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:37.416][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 04:34:37.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 04:34:37.419][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 04:34:37.420][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:37.422][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:37.422][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:37.422][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:37.423][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 04:34:37.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:37.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:37.427][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:37.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:37.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:37.430][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:37.432][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:37.432][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 04:34:37.433][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:37.434][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:37.435][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:37.436][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 04:34:37.436][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 04:34:37.438][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:37.440][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:37.442][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 04:34:37.444][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:37.446][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:37.448][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:37.452][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 04:34:37.453][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 04:34:37.455][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 04:34:37.457][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 04:34:37.458][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:37.459][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:37.461][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 04:34:37.462][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 04:34:37.464][biodb::testThat]
biodb.INFO [2025-04-01 04:34:37.465][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-04-01 04:34:37.466][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:37.467][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:37.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 04:34:37.476][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:37.477][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:37.479][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-04-01 04:34:38.347][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-04-01 04:34:39.363][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:39.366][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-04-01 04:34:39.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-04-01 04:34:39.376][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:39.380][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:39.382][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:39.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:40.207][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:41.030][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:41.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-04-01 04:34:41.039][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-04-01 04:34:41.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:41.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:41.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:41.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:41.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:41.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:41.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:41.060][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[2025-04-01 04:34:41.065][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:41.067][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:41.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:41.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:42.718][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:42.720][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-04-01 04:34:42.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-04-01 04:34:42.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.781][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.DEBUG[2025-04-01 04:34:42.788][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:42.793][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:42.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-01 04:34:42.797][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:42.798][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-01 04:34:42.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.816][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:42.821][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:42.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-01 04:34:42.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:42.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-01 04:34:42.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:42.884][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:42.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-04-01 04:34:42.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:42.889][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-04-01 04:34:42.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.906][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:42.910][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:42.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-04-01 04:34:42.914][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:42.915][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-04-01 04:34:42.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:42.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:42.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:42.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:42.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:42.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:42.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:42.932][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:42.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:42.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:42.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:43.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:46.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:46.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-04-01 04:34:46.747][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-04-01 04:34:46.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:46.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:46.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:46.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:46.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:46.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:46.764][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.INFO [2025-04-01 04:34:46.773][biodb::testThat]
biodb.INFO [2025-04-01 04:34:46.774][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-04-01 04:34:46.776][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:46.777][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:46.782][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[2025-04-01 04:34:46.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:46.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:46.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:47.693][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:48.516][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:48.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-04-01 04:34:48.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-04-01 04:34:48.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:48.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:48.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:48.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:48.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:48.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:48.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:48.546][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:48.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:48.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:48.554][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:49.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:50.204][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:50.207][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-04-01 04:34:50.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-04-01 04:34:50.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:50.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 04:34:50.236][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 04:34:50.238][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 04:34:50.239][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 04:34:50.241][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 04:34:50.242][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.245][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.247][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.249][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.INFO [2025-04-01 04:34:50.254][biodb::testContext]
biodb.INFO [2025-04-01 04:34:50.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:50.256][biodb::testContext] Test context - Test web services
biodb.INFO [2025-04-01 04:34:50.258][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:50.259][biodb::testContext]
biodb.INFO [2025-04-01 04:34:50.262][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:50.265][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:50.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:50.271][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 04:34:50.272][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.278][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 04:34:50.279][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.284][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 04:34:50.286][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.291][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 04:34:50.293][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 04:34:50.294][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 04:34:50.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.300][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 04:34:50.301][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 04:34:50.303][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.308][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 04:34:50.310][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 04:34:50.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.315][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 04:34:50.317][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 04:34:50.319][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 04:34:50.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.325][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 04:34:50.326][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.332][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 04:34:50.334][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 04:34:50.335][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 04:34:50.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.341][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:50.343][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 04:34:50.344][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 04:34:50.346][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 04:34:50.347][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 04:34:50.349][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 04:34:50.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.353][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[2025-04-01 04:34:50.355][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 04:34:50.356][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 04:34:50.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.362][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 04:34:50.364][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 04:34:50.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.368][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[2025-04-01 04:34:50.370][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 04:34:50.371][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 04:34:50.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.377][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 04:34:50.379][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 04:34:50.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.383][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[2025-04-01 04:34:50.385][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 04:34:50.386][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 04:34:50.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.392][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:50.393][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 04:34:50.398][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 04:34:50.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.403][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 04:34:50.405][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 04:34:50.406][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 04:34:50.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.412][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 04:34:50.415][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.416][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-01 04:34:50.418][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.419][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:50.421][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.422][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:50.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:50.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.431][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 04:34:50.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:50.434][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.435][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.437][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:50.437][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:50.437][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:50.437][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:50.437][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:50.438][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:50.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.443][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:50.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.448][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:50.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:50.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.454][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.456][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 04:34:50.459][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.460][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:50.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:50.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.470][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.471][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:50.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:50.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.476][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 04:34:50.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:50.479][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.482][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:50.482][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:50.482][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:50.482][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:50.482][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:50.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:50.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.488][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:50.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.494][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.496][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:50.497][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:50.499][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.500][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.502][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 04:34:50.505][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.507][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-01 04:34:50.508][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.521][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:50.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.537][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.540][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:50.542][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:50.543][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.545][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 04:34:50.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:50.548][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.550][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.551][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.553][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:50.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:50.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.561][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.563][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.564][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:50.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:50.567][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.569][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.571][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 04:34:50.573][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.575][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:50.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:50.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.583][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.584][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.586][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:50.587][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:50.589][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.590][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 04:34:50.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:50.594][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:50.597][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.598][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:50.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:50.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:50.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:50.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:50.608][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:50.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:50.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:50.614][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:50.616][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:50.617][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.618][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.DEBUG[2025-04-01 04:34:50.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.645][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[2025-04-01 04:34:50.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.652][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[2025-04-01 04:34:50.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.694][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[2025-04-01 04:34:50.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.700][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[2025-04-01 04:34:50.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.713][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[2025-04-01 04:34:50.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.719][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[2025-04-01 04:34:50.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.725][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[2025-04-01 04:34:50.726][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 04:34:50.728][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 04:34:50.730][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 04:34:50.732][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 04:34:50.734][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:50.736][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 04:34:50.738][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:50.740][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:50.742][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 04:34:50.744][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 04:34:50.746][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:50.747][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 04:34:50.749][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:50.751][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:50.753][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 04:34:50.755][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 04:34:50.757][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 04:34:50.759][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 04:34:50.761][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:50.763][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 04:34:50.765][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 04:34:50.767][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 04:34:50.769][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 04:34:50.771][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 04:34:50.772][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 04:34:50.774][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 04:34:50.776][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 04:34:50.778][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 04:34:50.780][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 04:34:50.782][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 04:34:50.784][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 04:34:50.786][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 04:34:50.788][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 04:34:50.790][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 04:34:50.792][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 04:34:50.794][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 04:34:50.795][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 04:34:50.797][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 04:34:50.799][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 04:34:50.801][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 04:34:50.803][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 04:34:50.805][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 04:34:50.807][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 04:34:50.809][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 04:34:50.811][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 04:34:50.813][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 04:34:50.815][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 04:34:50.817][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 04:34:50.819][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 04:34:50.821][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 04:34:50.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 04:34:50.824][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 04:34:50.826][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 04:34:50.828][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 04:34:50.830][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 04:34:50.832][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 04:34:50.834][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 04:34:50.836][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 04:34:50.838][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 04:34:50.840][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 04:34:50.842][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 04:34:50.844][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 04:34:50.846][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 04:34:50.848][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 04:34:50.849][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 04:34:50.851][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 04:34:50.853][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:50.855][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:50.857][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 04:34:50.859][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 04:34:50.861][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 04:34:50.863][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 04:34:50.865][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 04:34:50.867][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 04:34:50.869][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 04:34:50.871][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 04:34:50.873][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 04:34:50.875][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 04:34:50.877][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 04:34:50.879][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 04:34:50.881][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 04:34:50.883][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 04:34:50.884][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 04:34:50.887][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 04:34:50.889][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:50.890][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:50.891][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.894][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.912][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[2025-04-01 04:34:50.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:50.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:50.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:50.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:50.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:50.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:50.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:50.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:51.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:51.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:51.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:51.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:51.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:51.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:51.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:51.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:51.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:51.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:51.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:51.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:51.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:51.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:51.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:51.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:51.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:51.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:51.045][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:51.046][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 04:34:51.049][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:51.050][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 04:34:51.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:51.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:51.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:51.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:51.057][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:51.058][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 04:34:51.059][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 04:34:51.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:51.062][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:51.063][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 04:34:51.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 04:34:51.066][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 04:34:51.067][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:51.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:51.068][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:51.068][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:51.070][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 04:34:51.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:51.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:51.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:51.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:51.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:51.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:51.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:51.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 04:34:51.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:51.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:51.082][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:51.083][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 04:34:51.083][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 04:34:51.085][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:51.087][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:51.089][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 04:34:51.091][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:51.093][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:51.095][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:51.099][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 04:34:51.101][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 04:34:51.102][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 04:34:51.104][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 04:34:51.106][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:51.107][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:51.109][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 04:34:51.110][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 04:34:51.112][biodb::testThat]
biodb.INFO [2025-04-01 04:34:51.113][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-04-01 04:34:51.114][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:51.115][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:51.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 04:34:51.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:51.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 04:34:51.127][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:51.129][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 04:34:51.134][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[2025-04-01 04:34:51.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:51.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:51.141][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-04-01 04:34:51.962][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-04-01 04:34:52.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:52.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-04-01 04:34:52.796][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-04-01 04:34:52.806][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 04:34:52.808][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 04:34:52.810][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 04:34:52.811][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 04:34:52.812][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:52.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:52.814][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:52.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:52.817][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-01 04:34:52.822][biodb::testContext]
biodb.INFO [2025-04-01 04:34:52.824][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:52.825][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-04-01 04:34:52.826][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-01 04:34:52.827][biodb::testContext]
biodb.INFO [2025-04-01 04:34:52.830][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:52.832][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:52.837][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:52.838][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-01 04:34:52.840][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.845][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-01 04:34:52.846][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.851][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-01 04:34:52.852][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.856][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[2025-04-01 04:34:52.857][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-01 04:34:52.859][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-01 04:34:52.860][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-01 04:34:52.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.865][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-01 04:34:52.867][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-01 04:34:52.868][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.872][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[2025-04-01 04:34:52.873][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-01 04:34:52.874][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-01 04:34:52.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.879][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-01 04:34:52.881][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-01 04:34:52.882][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-01 04:34:52.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.887][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-01 04:34:52.888][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.893][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-01 04:34:52.894][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-01 04:34:52.896][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-01 04:34:52.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.900][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:52.902][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-01 04:34:52.903][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-01 04:34:52.904][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-01 04:34:52.906][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-01 04:34:52.907][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-01 04:34:52.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.912][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-01 04:34:52.913][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-01 04:34:52.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.918][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-01 04:34:52.920][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-01 04:34:52.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.926][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-01 04:34:52.927][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-01 04:34:52.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.932][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-01 04:34:52.933][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-01 04:34:52.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.938][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-01 04:34:52.940][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-01 04:34:52.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.945][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-01 04:34:52.946][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-01 04:34:52.951][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-01 04:34:52.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.957][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-01 04:34:52.958][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-01 04:34:52.959][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-01 04:34:52.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:52.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:52.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:52.965][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-01 04:34:52.968][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:52.969][self$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[2025-04-01 04:34:52.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:52.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:52.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:52.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:52.976][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:52.977][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:52.978][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:52.980][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:52.981][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:52.983][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-01 04:34:52.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:52.985][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:52.987][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:52.988][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:52.988][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:52.988][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:52.988][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:52.988][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:52.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:52.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:52.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:52.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:52.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:52.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:52.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:52.998][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:53.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:53.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.003][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.005][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-01 04:34:53.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:53.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:53.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:53.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:53.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.023][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-01 04:34:53.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:53.026][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.027][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.036][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:53.036][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:53.036][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:53.036][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-01 04:34:53.036][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-01 04:34:53.042][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:53.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:53.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.049][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.051][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:53.053][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:53.054][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.056][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.057][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-01 04:34:53.059][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.061][self$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[2025-04-01 04:34:53.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:53.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.066][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.067][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.070][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-01 04:34:53.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:53.073][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.074][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-01 04:34:53.075][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:53.077][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.078][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.079][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.081][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:53.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:53.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.090][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:53.092][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:53.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.095][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.096][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-01 04:34:53.099][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.100][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-01 04:34:53.101][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.103][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:53.104][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.105][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.108][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.109][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-01 04:34:53.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:53.112][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.113][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-01 04:34:53.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:53.116][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.117][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.118][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-01 04:34:53.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:53.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.129][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:53.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:53.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.134][self$setPropertyValue]
biodb.DEBUG[2025-04-01 04:34:53.135][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:53.136][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.143][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[2025-04-01 04:34:53.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.149][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[2025-04-01 04:34:53.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.190][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[2025-04-01 04:34:53.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.208][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[2025-04-01 04:34:53.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.240][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-01 04:34:53.242][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-01 04:34:53.244][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-01 04:34:53.246][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-01 04:34:53.247][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:53.249][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-01 04:34:53.251][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:53.253][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:53.255][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-01 04:34:53.257][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-01 04:34:53.259][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:53.261][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-01 04:34:53.263][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-01 04:34:53.265][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-01 04:34:53.267][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-01 04:34:53.269][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-01 04:34:53.271][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-01 04:34:53.273][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-01 04:34:53.275][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:53.277][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-01 04:34:53.279][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-01 04:34:53.281][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-01 04:34:53.283][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-01 04:34:53.285][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-01 04:34:53.287][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-01 04:34:53.289][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-01 04:34:53.291][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-01 04:34:53.293][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-01 04:34:53.295][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-01 04:34:53.296][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-01 04:34:53.298][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-01 04:34:53.300][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-01 04:34:53.302][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-01 04:34:53.304][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-01 04:34:53.306][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-01 04:34:53.308][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-01 04:34:53.310][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-01 04:34:53.312][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-01 04:34:53.314][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-01 04:34:53.316][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-01 04:34:53.318][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-01 04:34:53.320][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-01 04:34:53.322][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-01 04:34:53.323][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-01 04:34:53.325][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-01 04:34:53.327][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-01 04:34:53.329][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-01 04:34:53.331][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-01 04:34:53.333][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-01 04:34:53.335][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-01 04:34:53.337][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-01 04:34:53.339][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-01 04:34:53.340][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-01 04:34:53.342][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-01 04:34:53.344][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-01 04:34:53.346][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-01 04:34:53.348][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-01 04:34:53.350][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-01 04:34:53.352][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-01 04:34:53.354][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-01 04:34:53.356][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-01 04:34:53.358][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-01 04:34:53.360][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-01 04:34:53.362][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-01 04:34:53.364][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-01 04:34:53.366][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-01 04:34:53.368][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:53.370][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:53.372][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-01 04:34:53.373][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-01 04:34:53.375][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-01 04:34:53.377][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-01 04:34:53.379][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-01 04:34:53.381][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-01 04:34:53.383][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-01 04:34:53.385][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-01 04:34:53.387][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-01 04:34:53.389][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-01 04:34:53.391][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-01 04:34:53.393][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-01 04:34:53.395][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-01 04:34:53.397][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-01 04:34:53.398][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-01 04:34:53.401][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-01 04:34:53.403][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-04-01 04:34:53.404][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-01 04:34:53.405][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.408][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.434][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.DEBUG[2025-04-01 04:34:53.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.467][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[2025-04-01 04:34:53.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.500][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[2025-04-01 04:34:53.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.524][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[2025-04-01 04:34:53.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-01 04:34:53.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.559][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.4.3/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-04-01 04:34:53.561][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-04-01 04:34:53.564][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.565][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.568][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-01 04:34:53.569][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.570][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.572][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.573][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-04-01 04:34:53.574][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-01 04:34:53.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-01 04:34:53.577][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.578][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-04-01 04:34:53.580][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-04-01 04:34:53.581][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-04-01 04:34:53.582][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-01 04:34:53.584][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-01 04:34:53.584][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-01 04:34:53.584][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-01 04:34:53.585][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-01 04:34:53.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.589][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-01 04:34:53.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-01 04:34:53.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-01 04:34:53.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-01 04:34:53.594][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:53.594][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-04-01 04:34:53.595][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-01 04:34:53.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-01 04:34:53.598][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-01 04:34:53.599][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-04-01 04:34:53.599][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-04-01 04:34:53.601][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-01 04:34:53.603][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-01 04:34:53.605][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-04-01 04:34:53.607][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-01 04:34:53.609][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-01 04:34:53.611][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-01 04:34:53.615][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-04-01 04:34:53.617][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-04-01 04:34:53.618][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-04-01 04:34:53.620][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-04-01 04:34:53.622][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:53.623][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-01 04:34:53.625][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-04-01 04:34:53.627][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-04-01 04:34:53.628][biodb::testThat]
biodb.INFO [2025-04-01 04:34:53.630][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-04-01 04:34:53.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-01 04:34:53.632][biodb::testThat]
biodb.DEBUG[2025-04-01 04:34:53.636][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-04-01 04:34:53.641][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:53.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-04-01 04:34:53.644][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:53.646][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-04-01 04:34:53.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-04-01 04:34:53.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-04-01 04:34:53.657][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-04-01 04:34:53.659][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-01 04:34:53.660][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-04-01 04:34:53.666][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-04-01 04:34:53.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-04-01 04:34:53.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-04-01 04:34:53.671][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-04-01 04:34:53.673][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-04-01 04:34:53.674][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-04-01 04:34:53.676][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-04-01 04:34:53.677][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-04-01 04:34:53.678][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-04-01 04:34:53.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:53.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:53.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:53.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:53.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:53.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:53.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-01 04:34:53.696][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-04-01 04:34:53.700][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-04-01 04:34:53.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-04-01 04:34:53.703][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-04-01 04:34:54.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-04-01 04:34:57.392][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-04-01 04:34:57.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-04-01 04:34:57.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-04-01 04:34:57.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-04-01 04:34:57.405][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-04-01 04:34:57.406][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-04-01 04:34:57.408][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-04-01 04:34:57.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-01 04:34:57.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:57.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:57.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:57.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:57.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:57.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-01 04:34:57.428][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.429][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.432][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.439][ef$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:57.441][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:57.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.444][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-04-01 04:34:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-04-01 04:34:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.451][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:57.453][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:57.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.455][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-01 04:34:57.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-01 04:34:57.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.463][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-01 04:34:57.464][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-01 04:34:57.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.467][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.469][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-01 04:34:57.470][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-01 04:34:57.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.473][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.475][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:57.476][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:57.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.479][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.481][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:57.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-01 04:34:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.487][ef$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:57.488][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:57.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.491][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.493][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-04-01 04:34:57.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-01 04:34:57.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.498][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:57.500][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:57.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.502][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-01 04:34:57.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.510][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:57.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:57.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.514][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-01 04:34:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-01 04:34:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.522][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:57.524][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:57.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.526][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-04-01 04:34:57.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-04-01 04:34:57.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:57.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:57.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.541][ef$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-01 04:34:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-01 04:34:57.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-01 04:34:57.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-01 04:34:57.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-01 04:34:57.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-01 04:34:57.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-01 04:34:57.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-01 04:34:57.614][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-04-01 04:34:57.618][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-01 04:34:57.620][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-04-01 04:34:57.622][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-04-01 04:34:57.623][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-01 04:34:57.624][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-01 04:34:57.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-01 04:34:57.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-01 04:34:57.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-01 04:34:57.628][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-01 04:34:57.630][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 379 ]
>
> proc.time()
user system elapsed
24.633 0.942 100.555
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.115 | 0.082 | 3.206 | |
| ChebiEntry | 0.213 | 0.000 | 0.213 | |