Pierrick Roger
| Snapshot Date: 2024-09-16 14:00 -0400 (Mon, 16 Sep 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: dfe3f6c |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-17 11:36 -0400 (Tue, 17 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 201/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz |
| StartedAt: 2024-09-16 22:03:54 -0400 (Mon, 16 Sep 2024) |
| EndedAt: 2024-09-16 22:05:45 -0400 (Mon, 16 Sep 2024) |
| EllapsedTime: 110.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-09-16 22:04:29.162][biodb::testContext]
biodb.INFO [2024-09-16 22:04:29.163][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:04:29.164][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-09-16 22:04:29.165][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:04:29.166][biodb::testContext]
biodb.INFO [2024-09-16 22:04:29.171][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:04:29.173][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-16 22:04:29.179][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:04:29.180][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-16 22:04:29.181][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.184][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-16 22:04:29.201][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.204][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-16 22:04:29.205][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.209][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-16 22:04:29.209][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-16 22:04:29.210][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-16 22:04:29.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.214][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-16 22:04:29.214][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-16 22:04:29.215][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.219][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-16 22:04:29.220][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-16 22:04:29.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.223][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-16 22:04:29.224][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-16 22:04:29.225][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-16 22:04:29.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.228][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-16 22:04:29.229][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.232][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-16 22:04:29.233][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-16 22:04:29.234][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-16 22:04:29.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.237][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:04:29.238][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-16 22:04:29.239][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-16 22:04:29.240][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-16 22:04:29.241][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-16 22:04:29.241][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-16 22:04:29.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.245][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-16 22:04:29.246][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-16 22:04:29.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.249][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-16 22:04:29.250][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-16 22:04:29.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.252][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[2024-09-16 22:04:29.253][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-16 22:04:29.254][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-16 22:04:29.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.257][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-16 22:04:29.258][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-16 22:04:29.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.261][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-16 22:04:29.262][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-16 22:04:29.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.265][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:04:29.266][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-16 22:04:29.270][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-16 22:04:29.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.273][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[2024-09-16 22:04:29.274][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-16 22:04:29.274][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-16 22:04:29.275][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-16 22:04:29.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.281][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-16 22:04:29.312][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.333][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-16 22:04:29.334][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:04:29.335][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.337][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.338][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:04:29.339][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:04:29.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.340][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-16 22:04:29.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:04:29.341][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.342][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:04:29.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:04:29.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:04:29.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.347][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.348][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.349][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:04:29.349][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:04:29.350][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.350][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.351][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-16 22:04:29.353][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.353][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:04:29.354][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.355][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:04:29.355][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.357][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.358][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:04:29.359][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:04:29.359][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.360][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-16 22:04:29.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:04:29.361][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:04:29.362][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:04:29.363][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:04:29.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.364][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:04:29.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.367][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.367][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.368][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:04:29.369][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:04:29.369][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.370][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.371][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-16 22:04:29.372][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.373][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-16 22:04:29.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:04:29.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:04:29.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:04:29.379][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.379][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-16 22:04:29.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:04:29.381][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.382][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:04:29.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.384][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:04:29.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.387][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:04:29.388][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:04:29.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.389][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.390][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-16 22:04:29.391][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.392][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:04:29.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:04:29.394][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.395][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.396][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.397][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:04:29.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:04:29.398][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.399][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-16 22:04:29.399][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:04:29.400][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.401][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.402][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:04:29.402][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:04:29.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.406][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.406][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.407][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:04:29.407][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:04:29.408][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.409][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:04:29.411][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:04:29.412][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.412][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[2024-09-16 22:04:29.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.462][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-16 22:04:29.466][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-16 22:04:29.466][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-16 22:04:29.467][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-16 22:04:29.468][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:04:29.469][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-16 22:04:29.470][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-16 22:04:29.471][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-16 22:04:29.472][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-16 22:04:29.473][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-16 22:04:29.474][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:04:29.475][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-16 22:04:29.476][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-16 22:04:29.477][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-16 22:04:29.478][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-16 22:04:29.479][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-16 22:04:29.479][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-16 22:04:29.480][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-16 22:04:29.481][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:04:29.482][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-16 22:04:29.483][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-16 22:04:29.484][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-16 22:04:29.485][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-16 22:04:29.486][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-16 22:04:29.487][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-16 22:04:29.488][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-16 22:04:29.489][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-16 22:04:29.490][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-16 22:04:29.491][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-16 22:04:29.492][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-16 22:04:29.493][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-16 22:04:29.493][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-16 22:04:29.494][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-16 22:04:29.495][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-16 22:04:29.496][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-16 22:04:29.497][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-16 22:04:29.498][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-16 22:04:29.499][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-16 22:04:29.504][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-16 22:04:29.505][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-16 22:04:29.506][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-16 22:04:29.507][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-16 22:04:29.508][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-16 22:04:29.509][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-16 22:04:29.510][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-16 22:04:29.511][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-16 22:04:29.512][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-16 22:04:29.513][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-16 22:04:29.514][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-16 22:04:29.515][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-16 22:04:29.516][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-16 22:04:29.517][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-16 22:04:29.518][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-16 22:04:29.519][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-16 22:04:29.520][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-16 22:04:29.521][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-16 22:04:29.521][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-16 22:04:29.522][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-16 22:04:29.523][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-16 22:04:29.524][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-16 22:04:29.525][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-16 22:04:29.526][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-16 22:04:29.527][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-16 22:04:29.528][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-16 22:04:29.529][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-16 22:04:29.530][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-16 22:04:29.531][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:04:29.532][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:04:29.533][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-16 22:04:29.534][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-16 22:04:29.535][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-16 22:04:29.536][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-16 22:04:29.537][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-16 22:04:29.538][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-16 22:04:29.538][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-16 22:04:29.539][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-16 22:04:29.540][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-16 22:04:29.541][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-16 22:04:29.542][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-16 22:04:29.543][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-16 22:04:29.544][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-16 22:04:29.545][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-16 22:04:29.546][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-16 22:04:29.550][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-16 22:04:29.551][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:04:29.553][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:04:29.554][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.555][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.571][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[2024-09-16 22:04:29.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.579][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[2024-09-16 22:04:29.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.595][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[2024-09-16 22:04:29.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.603][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[2024-09-16 22:04:29.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.612][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[2024-09-16 22:04:29.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.616][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[2024-09-16 22:04:29.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:04:29.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:29.630][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-16 22:04:29.637][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-16 22:04:29.638][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.639][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:04:29.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.642][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.643][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-16 22:04:29.644][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-16 22:04:29.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:04:29.645][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.646][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-16 22:04:29.646][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-16 22:04:29.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-16 22:04:29.648][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-16 22:04:29.649][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:04:29.649][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:04:29.649][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:04:29.649][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-16 22:04:29.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.651][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:04:29.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:04:29.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:04:29.653][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:04:29.654][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:29.654][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-16 22:04:29.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:04:29.655][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:04:29.655][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-16 22:04:29.656][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-16 22:04:29.656][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-16 22:04:29.660][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:04:29.661][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:04:29.662][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-16 22:04:29.663][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:04:29.664][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:04:29.665][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:04:29.684][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-16 22:04:29.685][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-16 22:04:29.688][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-16 22:04:29.690][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-16 22:04:29.693][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:04:29.694][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:04:29.695][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-16 22:04:29.695][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-16 22:04:29.702][biodb::testThat]
biodb.INFO [2024-09-16 22:04:29.702][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-09-16 22:04:29.703][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:29.704][biodb::testThat]
biodb.TRACE[2024-09-16 22:04:29.707][loadFileContents] Loaded 1 files from cache: [1]: "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-09-16 22:04:29.708][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:29.711][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:29.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:29.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:29.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:29.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:29.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:29.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:29.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:29.735][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.736][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.737][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.749][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:29.750][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:29.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:29.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:29.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.773][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:29.774][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:29.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.775][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:29.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:29.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.781][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:29.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.784][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.785][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.787][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.790][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:29.791][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:29.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.792][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.793][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:29.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.796][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:29.797][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.798][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:29.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:29.802][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:29.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.804][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:29.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:29.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.807][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:29.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:29.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.809][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:29.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:29.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.813][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:29.814][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:29.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.815][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.816][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:29.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:29.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:29.820][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:29.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.821][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:29.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:29.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:29.884][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-09-16 22:04:29.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:29.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:29.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:29.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:29.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:29.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:29.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:29.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:29.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:29.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:29.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:29.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:29.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:29.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:29.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:29.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.994][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.996][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:29.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:29.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:29.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:29.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.036][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.037][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.038][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.055][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.057][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.073][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.075][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.091][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.092][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.093][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.109][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.122][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.128][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.128][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.129][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.130][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.140][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.146][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.146][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.148][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.148][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.156][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.158][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.164][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.166][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.166][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.174][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.183][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.188][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.189][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.205][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.207][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.233][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.234][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.235][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.238][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.239][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.240][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.243][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.244][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.245][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.248][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.249][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.250][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.253][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.255][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.258][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.260][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.263][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.265][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.268][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.269][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.270][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.273][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.274][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.275][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.278][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.280][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.283][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.284][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.285][ef$get] fields variable is a list.
biodb.INFO [2024-09-16 22:04:30.290][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.291][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-16 22:04:30.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.292][biodb::testThat]
biodb.DEBUG[2024-09-16 22:04:30.302][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-09-16 22:04:30.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:30.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-09-16 22:04:30.311][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:30.312][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-09-16 22:04:30.312][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:30.329][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:30.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:30.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:30.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:30.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:30.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:30.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:30.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:30.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:30.343][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.344][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.346][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.361][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.362][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.363][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:30.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:30.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.367][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.367][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.369][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:30.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:30.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.372][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.373][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.374][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.378][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.378][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.380][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.383][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.384][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.385][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.386][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:30.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.389][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:30.389][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.391][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:30.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.396][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.400][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.400][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.402][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.405][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:30.406][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.407][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.408][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:30.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:30.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.411][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.411][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.413][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.414][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:30.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:30.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:30.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:30.443][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-09-16 22:04:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-16 22:04:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-16 22:04:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-16 22:04:30.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-16 22:04:30.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-16 22:04:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-16 22:04:30.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:04:30.457][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.457][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-16 22:04:30.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.459][biodb::testThat]
biodb.TRACE[2024-09-16 22:04:30.461][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.463][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:30.463][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-09-16 22:04:30.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:30.496][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-09-16 22:04:30.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-16 22:04:30.513][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:30.524][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-16 22:04:30.525][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:30.526][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-16 22:04:30.542][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[2024-09-16 22:04:30.544][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:30.545][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:04:30.545][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:30.548][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-16 22:04:30.549][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-09-16 22:04:30.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.557][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:30.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.559][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.559][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.560][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.561][ef$get] fields variable is a list.
biodb.INFO [2024-09-16 22:04:30.564][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.565][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-09-16 22:04:30.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.566][biodb::testThat]
biodb.TRACE[2024-09-16 22:04:30.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:30.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:30.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:30.632][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[2024-09-16 22:04:30.634][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:30.635][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:04:30.636][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:30.637][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-09-16 22:04:30.647][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.648][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-09-16 22:04:30.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.649][biodb::testThat]
biodb.TRACE[2024-09-16 22:04:30.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:30.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:30.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:30.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:30.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.720][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-16 22:04:30.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.722][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:30.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-16 22:04:30.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:30.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:30.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-16 22:04:30.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:30.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:04:30.731][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.732][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-16 22:04:30.732][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.733][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.738][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.739][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-16 22:04:30.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.740][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.745][biodb::testThat]
biodb.INFO [2024-09-16 22:04:30.746][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-16 22:04:30.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:30.747][biodb::testThat]
biodb.DEBUG[2024-09-16 22:04:30.750][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-09-16 22:04:31.466][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-09-16 22:04:32.349][biodb::testThat]
biodb.INFO [2024-09-16 22:04:32.350][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-16 22:04:32.350][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:32.351][biodb::testThat]
biodb.DEBUG[2024-09-16 22:04:32.786][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[2024-09-16 22:04:33.223][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:33.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:33.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.225][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.226][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:33.227][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:33.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.228][ef$get] fields variable is a list.
biodb.INFO [2024-09-16 22:04:33.230][biodb::testThat]
biodb.INFO [2024-09-16 22:04:33.230][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-09-16 22:04:33.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:04:33.232][biodb::testThat]
biodb.TRACE[2024-09-16 22:04:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:33.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:33.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:33.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:33.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:33.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:33.317][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[2024-09-16 22:04:33.320][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:33.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:04:33.321][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:33.322][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-16 22:04:33.365][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[2024-09-16 22:04:33.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:33.368][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:04:33.369][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:33.370][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-09-16 22:04:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-16 22:04:33.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-16 22:04:33.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:33.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:33.403][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[2024-09-16 22:04:33.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:33.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-16 22:04:33.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:33.411][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-16 22:04:33.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:33.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:33.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:33.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:33.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:33.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:33.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:33.420][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-09-16 22:04:33.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:33.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-09-16 22:04:33.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:33.461][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:33.462][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:33.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:33.463][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:33.464][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:33.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:33.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:33.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:33.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:33.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:33.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:33.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:33.473][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-09-16 22:04:33.475][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:33.476][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:33.477][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-09-16 22:04:33.876][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-09-16 22:04:34.279][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:34.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-09-16 22:04:34.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-09-16 22:04:34.294][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-09-16 22:04:34.295][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:34.296][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:34.296][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:34.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:34.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:34.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:34.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:34.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:34.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:34.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:34.306][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.308][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.311][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:34.312][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:34.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.313][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.314][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:34.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:34.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.317][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:34.318][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:34.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.319][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:34.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:34.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.323][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:34.324][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:34.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.325][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:34.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:34.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.329][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:34.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:34.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.331][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:34.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:34.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.334][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:34.335][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:34.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.336][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.337][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:34.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.339][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.347][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:34.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:34.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:34.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.352][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:34.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:34.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.356][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:34.357][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:34.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.358][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:34.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:34.363][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:34.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.364][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:34.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:34.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.367][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:34.368][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:34.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.369][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:34.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:34.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:34.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:34.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:34.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:34.400][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-09-16 22:04:34.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:34.416][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[2024-09-16 22:04:34.418][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:34.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-16 22:04:34.420][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:34.422][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-16 22:04:34.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:34.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:34.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:34.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:34.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:34.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:34.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:34.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:34.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:34.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:34.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:34.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:34.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:34.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:34.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:34.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:34.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:34.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:34.456][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-09-16 22:04:34.456][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:34.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-09-16 22:04:34.458][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:34.459][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:34.460][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:34.460][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:34.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:34.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:34.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:34.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:34.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:34.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:34.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:34.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:34.483][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[2024-09-16 22:04:34.484][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-09-16 22:04:34.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:34.495][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:34.506][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-09-16 22:04:35.439][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-09-16 22:04:35.840][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:35.841][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-09-16 22:04:35.844][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-09-16 22:04:35.845][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-09-16 22:04:35.846][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:35.847][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:35.848][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:35.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:35.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:35.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:35.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:35.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:35.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:35.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:35.857][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.859][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.863][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:35.864][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:35.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.865][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.866][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:35.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:35.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.869][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:35.869][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:35.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.871][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:35.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:35.875][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:35.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.876][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:35.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:35.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.880][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:35.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:35.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.882][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:35.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:35.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.886][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:35.886][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:35.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.888][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.888][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:35.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.890][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:35.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.894][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:35.895][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:35.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.896][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:35.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:35.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.900][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:35.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:35.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.902][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:35.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:35.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.905][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:35.906][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:35.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.907][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.908][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:35.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:35.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:35.912][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:35.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.913][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:35.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:35.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:35.952][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-09-16 22:04:35.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:35.973][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[2024-09-16 22:04:35.976][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:04:35.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:04:35.978][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:04:35.979][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-16 22:04:35.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:35.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:35.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:35.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:35.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:35.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:35.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:35.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:35.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:35.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:35.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:35.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:35.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:36.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:36.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:36.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:36.003][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[2024-09-16 22:04:36.003][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-09-16 22:04:36.004][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:36.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-09-16 22:04:36.006][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:36.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:36.008][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:36.008][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:36.009][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:36.010][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:36.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:36.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:36.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:36.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:36.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:36.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:36.018][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[2024-09-16 22:04:36.018][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-09-16 22:04:36.020][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:36.021][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:36.022][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-09-16 22:04:36.423][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-09-16 22:04:36.821][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:36.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-09-16 22:04:36.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-09-16 22:04:36.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-09-16 22:04:36.828][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:36.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:36.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:36.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:36.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:36.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:36.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:36.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:36.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:36.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:36.839][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.841][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.851][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:36.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:36.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.853][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.854][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:36.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:36.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.856][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:36.858][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:36.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.859][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.860][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:36.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:36.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.862][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.863][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:36.864][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:36.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.865][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.866][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:36.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.868][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.869][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:36.870][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:36.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.871][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:36.872][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:36.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.874][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:36.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:36.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.877][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:36.878][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:36.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.879][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.880][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:36.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:36.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.883][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:36.884][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:36.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.885][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:36.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:36.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:36.913][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-09-16 22:04:36.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:36.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:36.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:36.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:36.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:36.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:36.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:36.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:36.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:36.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:36.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:36.935][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-09-16 22:04:36.936][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:36.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-09-16 22:04:36.938][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:36.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:36.940][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:36.940][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:36.941][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:36.942][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:36.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:36.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:36.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:36.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:36.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:36.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:36.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:36.951][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-09-16 22:04:36.953][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:36.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:36.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-09-16 22:04:37.353][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-09-16 22:04:37.753][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-09-16 22:04:37.755][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-09-16 22:04:37.756][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-09-16 22:04:37.758][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-09-16 22:04:37.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-09-16 22:04:37.761][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:37.762][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:37.763][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:37.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:37.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:37.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:37.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:37.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:37.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:37.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:37.780][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.782][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.786][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:37.787][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:37.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.789][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:37.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:37.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.791][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:37.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:37.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.794][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:37.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:37.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.797][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.798][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:37.799][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:37.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.800][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.801][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:37.802][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.803][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:37.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:37.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.806][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.807][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:37.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:37.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.809][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:37.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.813][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:37.813][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:37.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.815][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.815][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.818][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:37.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:37.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.820][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:37.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:37.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:37.848][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-09-16 22:04:37.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:37.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:37.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:37.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:37.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:37.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:37.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:37.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:37.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:37.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:37.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:37.870][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-09-16 22:04:37.871][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:37.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-09-16 22:04:37.873][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:37.874][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:37.874][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:37.875][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:37.876][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:37.876][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:37.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:37.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:37.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:37.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:37.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:37.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:37.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:37.886][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-09-16 22:04:37.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:37.888][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:37.889][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-09-16 22:04:38.398][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-09-16 22:04:38.797][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:38.799][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-09-16 22:04:38.801][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-09-16 22:04:38.809][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-09-16 22:04:38.810][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:38.811][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:38.812][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:38.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:38.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:38.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:38.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:38.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:38.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:38.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:38.822][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.824][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.827][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:38.828][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:38.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.830][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.830][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:38.831][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:38.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.833][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:38.834][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:38.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.835][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.836][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:38.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:38.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.838][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.839][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:38.840][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:38.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.841][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.842][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:38.843][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.844][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.845][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:38.846][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:38.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.847][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.848][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:38.848][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:38.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.850][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:38.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.854][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:38.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:38.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.856][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:38.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:38.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.859][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:38.860][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:38.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.861][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:38.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:38.890][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-09-16 22:04:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:38.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:38.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:38.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:38.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:38.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:38.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:38.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:38.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:38.912][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-09-16 22:04:38.912][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:38.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-09-16 22:04:38.914][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:38.915][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:38.916][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:38.917][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:38.917][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:38.918][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:38.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:38.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:38.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:38.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:38.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:38.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:38.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:38.927][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-09-16 22:04:38.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:38.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:38.935][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-09-16 22:04:39.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-09-16 22:04:39.739][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-09-16 22:04:39.740][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-09-16 22:04:39.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-09-16 22:04:39.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-09-16 22:04:39.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-09-16 22:04:39.747][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:39.748][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:39.748][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:39.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:39.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:39.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:39.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:39.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:39.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:39.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:39.758][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.760][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.763][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:39.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:39.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.765][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.766][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:39.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:39.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.769][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:39.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:39.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.771][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:39.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:39.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.775][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:39.775][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:39.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.777][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:39.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:39.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:39.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:39.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.782][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:39.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:39.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:39.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:39.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.789][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:39.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:39.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.792][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:39.792][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.794][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:39.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:39.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.799][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:39.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:39.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.803][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:39.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:39.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.805][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.809][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:39.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:39.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.811][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.811][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:39.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:39.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.814][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:39.815][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:39.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.816][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.817][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:39.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:39.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:39.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:39.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:39.847][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-09-16 22:04:39.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:39.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:39.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:39.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:39.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:39.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:39.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:39.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:39.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:39.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:39.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:39.871][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-09-16 22:04:39.872][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:39.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-09-16 22:04:39.874][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:39.875][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:39.876][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:39.876][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:39.877][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:39.878][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:39.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:39.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:39.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:39.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:39.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:39.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:39.886][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[2024-09-16 22:04:39.887][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-09-16 22:04:39.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:39.889][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:39.890][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-09-16 22:04:40.297][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-09-16 22:04:40.701][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:40.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-09-16 22:04:40.705][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-09-16 22:04:40.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-09-16 22:04:40.708][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:40.709][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:40.710][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:40.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:40.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:40.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:40.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:40.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:40.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:40.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:40.719][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.721][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.725][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:40.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:40.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.727][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.728][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:40.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:40.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.730][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:40.731][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:40.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.732][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:40.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:40.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:40.737][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:40.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.738][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.742][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:40.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:40.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.744][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:40.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:40.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.747][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:40.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:40.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.749][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.750][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:40.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:40.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.753][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:40.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.755][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:40.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.758][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:40.759][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:40.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.760][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:40.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:40.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.764][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:40.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:40.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.766][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:40.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:40.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.770][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:40.770][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:40.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.772][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.775][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:40.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:40.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.777][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:40.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:40.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:40.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:40.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:40.816][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-09-16 22:04:40.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:40.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:40.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:40.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:40.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:40.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:40.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:40.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:40.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:40.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:40.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:40.832][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-09-16 22:04:40.833][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:40.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-09-16 22:04:40.835][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:40.836][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:40.837][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:40.837][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:40.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:40.839][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:40.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:40.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:40.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:40.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:40.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:40.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:40.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:40.848][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-09-16 22:04:40.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:40.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:40.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-09-16 22:04:41.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-09-16 22:04:41.646][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:41.648][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-09-16 22:04:41.650][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-09-16 22:04:41.652][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-09-16 22:04:41.653][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:41.653][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:41.654][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:41.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:41.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:41.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:41.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:41.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:41.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:41.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:41.663][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.665][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.669][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:41.670][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:41.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.671][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:41.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:41.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.675][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:41.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:41.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.677][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:41.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:41.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:41.681][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:41.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.682][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:41.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:41.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.686][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:41.686][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:41.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.688][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:41.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:41.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:41.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:41.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.693][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.694][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:41.695][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.696][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.697][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:41.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.700][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:41.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:41.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.702][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:41.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.705][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:41.706][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:41.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.707][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:41.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:41.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.718][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:41.719][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:41.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.720][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.721][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:41.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.724][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:41.724][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:41.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.726][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.727][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:41.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:41.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:41.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:41.756][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-09-16 22:04:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:41.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:41.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:41.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:41.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:41.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:41.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:41.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:41.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:41.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:41.772][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-09-16 22:04:41.773][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:41.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-09-16 22:04:41.775][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:41.776][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:41.777][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:41.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:41.778][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:41.779][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:41.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:41.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:41.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:41.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:41.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:41.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:41.787][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[2024-09-16 22:04:41.788][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-09-16 22:04:41.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:41.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:41.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-09-16 22:04:42.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-09-16 22:04:42.799][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:42.801][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-09-16 22:04:42.803][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-09-16 22:04:42.805][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-09-16 22:04:42.806][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:42.807][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:42.807][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:42.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:42.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:42.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:42.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:42.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:42.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:42.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:42.817][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.819][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.822][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:42.823][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:42.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.824][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.825][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:42.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:42.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.828][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:42.829][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:42.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.830][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:42.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:42.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.834][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:42.834][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:42.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.836][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:42.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:42.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.839][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:42.840][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:42.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.841][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:42.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:42.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:42.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:42.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.855][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.856][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:42.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.858][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.859][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:42.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.862][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:42.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:42.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.864][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:42.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:42.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.867][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:42.868][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:42.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.869][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:42.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:42.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.873][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:42.874][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:42.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.875][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.876][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:42.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:42.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.879][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:42.880][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:42.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.881][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:42.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:42.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:42.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:42.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:42.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:42.912][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-09-16 22:04:42.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:42.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:42.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:42.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:42.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:42.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:42.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:42.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:42.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:42.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:42.928][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-09-16 22:04:42.929][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:42.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-09-16 22:04:42.931][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:42.932][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:42.932][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:42.933][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:42.934][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:42.934][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:42.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:42.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:42.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:42.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:42.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:42.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:42.943][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[2024-09-16 22:04:42.943][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-09-16 22:04:42.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:42.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:42.947][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-09-16 22:04:43.347][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-09-16 22:04:43.747][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:43.749][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-09-16 22:04:43.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-09-16 22:04:43.753][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-09-16 22:04:43.754][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:43.755][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:43.756][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:43.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:43.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:43.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:43.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:43.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:43.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:43.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:43.766][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.768][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.780][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:43.781][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:43.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.782][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.783][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:43.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:43.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.786][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:43.787][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:43.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.788][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:43.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:43.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:43.792][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:43.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.794][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:43.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.797][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:43.798][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:43.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.799][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:43.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:43.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.803][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:43.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:43.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.805][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.806][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:43.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.808][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.809][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:43.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:43.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:43.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.814][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:43.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:43.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.817][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:43.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:43.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.819][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:43.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:43.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:43.824][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:43.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.825][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:43.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:43.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:43.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.830][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:43.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:43.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:43.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:43.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:43.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:43.861][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-09-16 22:04:43.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:43.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:43.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:43.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:43.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:43.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:43.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:43.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:43.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:43.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:43.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:43.878][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-09-16 22:04:43.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:43.879][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-09-16 22:04:43.880][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:43.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:43.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:43.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:43.883][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:43.884][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:43.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:43.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:43.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:43.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:43.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:43.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:43.892][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[2024-09-16 22:04:43.893][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-09-16 22:04:43.895][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:43.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:43.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-09-16 22:04:44.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-09-16 22:04:44.701][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:44.702][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-09-16 22:04:44.705][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-09-16 22:04:44.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-09-16 22:04:44.708][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:44.709][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:44.709][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:44.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:44.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:44.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:44.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:44.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:44.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:44.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:44.719][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.719][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.721][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.724][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:44.725][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:44.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.726][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.727][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:44.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:44.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.730][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:44.731][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:44.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.732][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:44.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:44.736][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:44.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.738][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:44.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:44.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.741][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:44.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:44.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.743][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:44.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.747][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:44.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:44.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.749][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.750][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:44.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.752][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:44.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.755][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:44.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:44.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.757][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:44.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.761][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:44.762][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:44.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.763][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:44.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:44.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.767][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:44.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:44.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.769][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:44.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:44.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.772][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:44.773][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:44.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.774][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:44.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:44.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:44.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:44.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:44.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:44.805][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-09-16 22:04:44.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:44.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:44.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:44.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:44.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:44.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:44.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:44.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:44.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:44.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:44.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:44.855][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-09-16 22:04:44.855][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:44.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-09-16 22:04:44.858][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:44.858][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:44.859][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:44.860][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:44.861][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:44.861][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:44.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:44.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:44.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:44.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:44.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:44.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:44.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:44.871][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-09-16 22:04:44.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:44.873][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:44.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-09-16 22:04:45.276][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-09-16 22:04:45.673][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:45.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-09-16 22:04:45.677][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-09-16 22:04:45.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-09-16 22:04:45.680][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:45.681][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:45.682][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:45.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:45.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:45.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:45.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:45.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:45.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:45.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:45.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.693][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.697][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:45.698][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:45.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.699][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.700][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:45.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.703][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:45.703][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:45.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.705][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:45.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:45.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.708][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:45.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:45.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.710][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:45.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:45.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.714][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:45.715][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:45.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.716][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:45.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.719][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:45.720][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:45.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.721][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.722][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:45.723][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.724][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.725][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:45.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.728][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:45.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:45.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.730][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:45.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:45.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.734][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:45.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:45.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.736][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:45.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:45.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.739][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:45.740][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:45.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.742][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.742][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:45.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:45.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.745][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:45.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:45.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.747][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.748][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:45.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:45.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:45.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:45.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:45.787][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-09-16 22:04:45.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:45.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:45.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:45.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:45.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:45.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:45.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:45.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:45.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:45.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:45.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:45.804][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-09-16 22:04:45.804][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:45.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-09-16 22:04:45.806][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:45.807][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:45.808][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:45.809][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:45.809][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:45.810][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:45.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:45.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:45.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:45.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:45.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:45.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:45.818][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.DEBUG[2024-09-16 22:04:45.819][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-09-16 22:04:45.821][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:45.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:45.823][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-09-16 22:04:46.224][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-09-16 22:04:46.627][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:46.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-09-16 22:04:46.632][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-09-16 22:04:46.634][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-09-16 22:04:46.635][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:46.636][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:46.637][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:46.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:46.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:46.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:46.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:46.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:46.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:46.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:46.647][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.648][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.649][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.653][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:46.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:46.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.655][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.656][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:46.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:46.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.659][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:46.660][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:46.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.661][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.662][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:46.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:46.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.665][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:46.665][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:46.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.667][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:46.668][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:46.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.670][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.671][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:46.671][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:46.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.673][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.673][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:46.674][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.675][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.679][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:46.680][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:46.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.681][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:46.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:46.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.685][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:46.686][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:46.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.687][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:46.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:46.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.690][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:46.691][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:46.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.692][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.693][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:46.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:46.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:46.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:46.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:46.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:46.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:46.736][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-09-16 22:04:46.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:46.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:46.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:46.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:46.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:46.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:46.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:46.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:46.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:46.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:46.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:46.753][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-09-16 22:04:46.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:46.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-09-16 22:04:46.756][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:46.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:46.758][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:46.759][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:46.759][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:46.760][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:46.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:46.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:46.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:46.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:46.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:46.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:46.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:46.769][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-09-16 22:04:46.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:46.772][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:46.773][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-09-16 22:04:47.174][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-09-16 22:04:47.574][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:47.576][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-09-16 22:04:47.579][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-09-16 22:04:47.581][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-09-16 22:04:47.582][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:47.582][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:47.583][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:47.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:47.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:47.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:47.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:47.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:47.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:47.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:47.593][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.595][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.599][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:47.599][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:47.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.601][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:47.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:47.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.605][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:47.605][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:47.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.607][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:47.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:47.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.610][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:47.611][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:47.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.612][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.613][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:47.614][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:47.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.615][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.616][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:47.617][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:47.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.618][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.619][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:47.619][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.621][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.621][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:47.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.624][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:47.625][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:47.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.626][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:47.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:47.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.630][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:47.630][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:47.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.632][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:47.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:47.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.635][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:47.636][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:47.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.645][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.646][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:47.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:47.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.649][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:47.650][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:47.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.651][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:47.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:47.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:47.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:47.679][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-09-16 22:04:47.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:47.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:47.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:47.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:47.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:47.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:47.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:47.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:47.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:47.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:47.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:47.696][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-09-16 22:04:47.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:47.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-09-16 22:04:47.698][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:47.699][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:47.700][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:47.701][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:47.701][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:47.702][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:47.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:47.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:47.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:47.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:47.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:47.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:47.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:47.711][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-09-16 22:04:47.713][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:47.713][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:47.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-09-16 22:04:48.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-09-16 22:04:48.515][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:48.517][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-09-16 22:04:48.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-09-16 22:04:48.521][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-09-16 22:04:48.522][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:48.523][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:48.524][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:48.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:48.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:48.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:48.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:48.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:48.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:48.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:48.534][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.536][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.540][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:48.540][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:48.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.542][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:48.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:48.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.545][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:48.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:48.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.547][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:48.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:48.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.551][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:48.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:48.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.553][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:48.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:48.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.556][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:48.557][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:48.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.558][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:48.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:48.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.562][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:48.563][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:48.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.564][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.573][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:48.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.575][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:48.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.579][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:48.580][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:48.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.581][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:48.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:48.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:48.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.587][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:48.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:48.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.591][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:48.591][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:48.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.593][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.594][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:48.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.596][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:48.597][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:48.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.598][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:48.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:48.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:48.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:48.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:48.629][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-09-16 22:04:48.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:48.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:48.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:48.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:48.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:48.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:48.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:48.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:48.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:48.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:48.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:48.645][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-09-16 22:04:48.646][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:48.647][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-09-16 22:04:48.648][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:48.649][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:48.649][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:48.650][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:48.651][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:48.652][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:48.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:48.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:48.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:48.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:48.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:48.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:48.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:48.661][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-09-16 22:04:48.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:48.663][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:48.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-09-16 22:04:49.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-09-16 22:04:49.486][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:49.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-09-16 22:04:49.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-09-16 22:04:49.492][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-09-16 22:04:49.493][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:49.494][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:49.495][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:49.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:49.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:49.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:49.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:49.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:49.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:49.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:49.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.506][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.507][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.510][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:49.511][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:49.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.512][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.513][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:49.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:49.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.524][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:49.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:49.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.526][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:49.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:49.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.530][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:49.531][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:49.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.532][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:49.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:49.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.536][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:49.537][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:49.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.538][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:49.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:49.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:49.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:49.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.544][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.544][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:49.545][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.546][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:49.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:49.551][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:49.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.552][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.556][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:49.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:49.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.558][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:49.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:49.562][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:49.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.563][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.564][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:49.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:49.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.567][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:49.568][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:49.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.569][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:49.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:49.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:49.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:49.599][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-09-16 22:04:49.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:49.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:49.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:49.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:49.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:49.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:49.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:49.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:49.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:49.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:49.616][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-09-16 22:04:49.616][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:49.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-09-16 22:04:49.618][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:49.619][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:49.620][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:49.621][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:49.621][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:49.622][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:49.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:49.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:49.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:49.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:49.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:49.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:49.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:49.631][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-09-16 22:04:49.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:49.633][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:49.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-09-16 22:04:50.047][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-09-16 22:04:50.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:50.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-09-16 22:04:50.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-09-16 22:04:50.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-09-16 22:04:50.463][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:50.464][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:50.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:50.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:50.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:50.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:50.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:50.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:50.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:50.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:50.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.477][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.481][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:50.482][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:50.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.483][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.484][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:50.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:50.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.487][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:50.488][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:50.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.489][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:50.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.493][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:50.493][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:50.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.494][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:50.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:50.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.498][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:50.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:50.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.500][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:50.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:50.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.504][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:50.504][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:50.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.506][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.506][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:50.507][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.508][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:50.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:50.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:50.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.514][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:50.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.517][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:50.518][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:50.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.519][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:50.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:50.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.523][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:50.524][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:50.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.525][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.526][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:50.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:50.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.529][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:50.529][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:50.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.531][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:50.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:50.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:50.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:50.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:50.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:50.562][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-09-16 22:04:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:50.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:50.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:50.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:50.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:50.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:50.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:50.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:50.578][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-09-16 22:04:50.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:50.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-09-16 22:04:50.585][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:50.586][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:50.587][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:50.588][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:50.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:50.590][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:50.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:50.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:50.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:50.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:50.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:50.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:50.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:50.599][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-09-16 22:04:50.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:50.601][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:50.602][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-09-16 22:04:51.002][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-09-16 22:04:51.401][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:51.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-09-16 22:04:51.406][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-09-16 22:04:51.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-09-16 22:04:51.409][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:51.410][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:51.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:51.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:51.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:51.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:51.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:51.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:51.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:51.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:51.420][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.422][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.426][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:51.427][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:51.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.428][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:51.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:51.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.432][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:51.432][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:51.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.434][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:51.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:51.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:51.438][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:51.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.439][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:51.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.443][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:51.444][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:51.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.445][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:51.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:51.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:51.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:51.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.450][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.451][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:51.452][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.453][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.454][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:51.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.457][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:51.458][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:51.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.459][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:51.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:51.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.463][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:51.463][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:51.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.465][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.468][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:51.469][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:51.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.470][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:51.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:51.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.474][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:51.475][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:51.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.476][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:51.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:51.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:51.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:51.515][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-09-16 22:04:51.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:51.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:51.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:51.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:51.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:51.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:51.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:51.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:51.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:51.532][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-09-16 22:04:51.533][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:51.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-09-16 22:04:51.535][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:51.536][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:51.537][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:51.537][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:51.538][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:51.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:51.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:51.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:51.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:51.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:51.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:51.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:51.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:51.548][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-09-16 22:04:51.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:51.550][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:51.551][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-09-16 22:04:51.951][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-09-16 22:04:52.822][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:52.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-09-16 22:04:52.828][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-09-16 22:04:52.830][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-09-16 22:04:52.831][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:52.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:52.833][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:52.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:52.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:52.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:52.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:52.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:52.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:52.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:52.843][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.845][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.849][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:52.850][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:52.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.851][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:52.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:52.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.855][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:52.856][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:52.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.857][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:52.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:52.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.860][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:52.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:52.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.862][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:52.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:52.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:52.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.868][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:52.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:52.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.872][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:52.872][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:52.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.874][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.875][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:52.875][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.877][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.877][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:52.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.880][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:52.881][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:52.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.882][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:52.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:52.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.886][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:52.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:52.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.888][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:52.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:52.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.892][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:52.892][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:52.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.894][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:52.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:52.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.897][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:52.898][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:52.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.899][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:52.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:52.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:52.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:52.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:52.940][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-09-16 22:04:52.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:52.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:52.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:52.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:52.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:52.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:52.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:52.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:52.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:52.957][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-09-16 22:04:52.957][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:52.958][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-09-16 22:04:52.959][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:52.960][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:52.961][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:52.962][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:52.962][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:52.963][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:52.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:52.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:52.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:52.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:52.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:52.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:52.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:52.972][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-09-16 22:04:52.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:52.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:52.976][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-09-16 22:04:53.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-09-16 22:04:53.776][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:53.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-09-16 22:04:53.784][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-09-16 22:04:53.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-09-16 22:04:53.792][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:53.793][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:53.794][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:53.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:53.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:53.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:53.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:53.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:53.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:53.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:53.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.809][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.813][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:53.814][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:53.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.815][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:53.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.819][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:53.820][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:53.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.821][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:53.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:53.825][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:53.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.827][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:53.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:53.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.830][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:53.831][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:53.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:53.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:53.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.836][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:53.837][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:53.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.838][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.839][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:53.839][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.841][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.841][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.844][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:53.845][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:53.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.846][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:53.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.859][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:53.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:53.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.861][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:53.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:53.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.865][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:53.866][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:53.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.867][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.871][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:53.872][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:53.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.873][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:53.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:53.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:53.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:53.904][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-09-16 22:04:53.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:53.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:53.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:53.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:53.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:53.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:53.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:53.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:53.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:53.920][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[2024-09-16 22:04:53.921][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-09-16 22:04:53.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:53.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-09-16 22:04:53.924][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:53.924][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:53.925][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:53.926][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:53.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:53.927][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:53.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:53.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:53.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:53.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:53.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:53.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:53.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:53.936][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-09-16 22:04:53.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:53.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:53.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-09-16 22:04:54.343][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-09-16 22:04:54.748][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:54.749][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-09-16 22:04:54.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-09-16 22:04:54.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-09-16 22:04:54.755][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:54.756][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:54.756][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:54.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:54.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:54.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:54.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:54.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:54.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:54.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:54.766][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.768][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.772][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:54.773][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:54.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.774][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:54.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.778][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:54.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:54.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.779][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:54.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:54.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.783][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:54.792][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:54.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.793][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:54.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:54.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.797][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:54.798][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:54.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.799][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.803][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:54.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:54.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.805][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.806][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:54.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.808][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.809][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:54.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:54.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:54.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.814][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.817][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:54.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:54.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.819][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:54.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:54.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.823][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:54.824][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:54.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.825][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:54.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:54.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.831][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:54.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:54.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:54.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:54.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:54.861][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-09-16 22:04:54.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:54.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:54.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:54.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:54.883][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[2024-09-16 22:04:54.885][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:54.886][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:54.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:04:55.417][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:04:55.982][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:55.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-09-16 22:04:55.987][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-09-16 22:04:55.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:55.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:55.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:55.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:55.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:55.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:55.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:55.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:55.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:56.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:56.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:56.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:56.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:56.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:56.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:56.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:56.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:56.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:56.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:56.617][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:04:56.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:56.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:56.627][private$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[2024-09-16 22:04:57.026][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[2024-09-16 22:04:57.426][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:57.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-09-16 22:04:57.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-09-16 22:04:57.433][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[2024-09-16 22:04:57.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:57.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:57.437][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:04:57.836][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:04:58.238][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:58.240][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-09-16 22:04:58.242][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-09-16 22:04:58.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:58.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:58.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:58.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:58.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:58.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:58.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:58.252][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-09-16 22:04:58.252][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:58.253][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-09-16 22:04:58.254][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:58.255][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:58.256][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:58.257][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:58.257][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:58.258][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:58.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:58.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:58.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:58.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:58.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:58.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:58.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:58.267][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-09-16 22:04:58.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:58.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:58.271][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-09-16 22:04:58.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-09-16 22:04:59.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:04:59.084][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-09-16 22:04:59.087][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-09-16 22:04:59.088][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-09-16 22:04:59.089][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:04:59.090][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:04:59.091][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:04:59.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:59.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:59.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:59.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:59.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:59.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:59.099][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.TRACE[2024-09-16 22:04:59.101][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.102][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.103][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.107][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:59.107][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:59.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.111][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.112][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:04:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:04:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.115][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:59.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:59.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.117][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:04:59.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:04:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:59.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:59.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.123][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:04:59.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:04:59.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:59.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:59.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.128][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:04:59.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:04:59.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:59.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:59.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.134][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:59.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:04:59.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.137][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:59.138][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:59.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.139][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.140][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:04:59.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:04:59.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.144][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.145][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.148][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:59.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:59.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.150][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:04:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:04:59.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.167][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:59.168][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:59.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.169][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.170][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:04:59.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:04:59.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:59.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:59.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.175][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:04:59.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:04:59.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:04:59.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:04:59.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:04:59.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:59.206][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-09-16 22:04:59.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:59.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:59.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:59.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:59.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:59.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:59.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:59.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:04:59.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:04:59.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:04:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:04:59.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:04:59.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:59.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:59.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:59.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:59.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:59.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:59.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:59.237][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-09-16 22:04:59.237][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:04:59.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-09-16 22:04:59.240][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:04:59.240][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:04:59.241][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:04:59.242][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:04:59.242][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:04:59.243][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:04:59.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:04:59.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:04:59.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:04:59.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:04:59.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:04:59.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:04:59.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:04:59.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-09-16 22:04:59.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:04:59.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:04:59.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-09-16 22:04:59.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-09-16 22:05:00.275][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:00.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-09-16 22:05:00.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-09-16 22:05:00.283][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-09-16 22:05:00.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:05:00.285][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:05:00.286][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:05:00.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.296][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.297][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.298][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.302][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:00.302][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:00.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.304][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.312][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:00.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.315][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:00.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:00.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.318][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:00.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:00.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:00.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:00.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.323][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:00.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:00.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:00.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:00.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.329][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:00.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.333][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:00.333][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:00.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.335][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.335][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:00.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:00.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.338][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.338][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:00.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:00.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.341][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.342][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.343][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.347][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:00.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:00.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.349][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:00.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:00.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.352][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:00.353][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:00.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.354][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:00.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:00.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:00.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.360][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:00.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:00.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:00.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.390][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-09-16 22:05:00.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:00.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:00.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:05:00.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:00.417][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-16 22:05:00.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.764][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:00.767][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:00.768][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-09-16 22:05:00.769][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:00.770][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-09-16 22:05:00.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:00.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:00.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:00.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:00.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:00.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:00.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:00.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:00.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:00.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:00.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:00.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:01.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:01.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:05:01.128][biodb::testThat]
biodb.INFO [2024-09-16 22:05:01.129][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-09-16 22:05:01.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:01.130][biodb::testThat]
biodb.TRACE[2024-09-16 22:05:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-16 22:05:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-16 22:05:01.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:01.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:01.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:01.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:01.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:01.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:01.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:01.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:01.156][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:01.159][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:01.159][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:01.161][private$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[2024-09-16 22:05:01.573][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[2024-09-16 22:05:01.980][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:01.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-09-16 22:05:01.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-09-16 22:05:02.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:02.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:02.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:02.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:02.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:02.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:02.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:02.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:02.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:02.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:02.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:02.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:02.020][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[2024-09-16 22:05:02.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:02.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:02.025][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:05:02.460][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:03.038][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:03.040][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-09-16 22:05:03.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-09-16 22:05:03.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:03.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:03.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:03.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:03.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:03.076][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:03.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:03.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.090][private$selectFields]
biodb.TRACE[2024-09-16 22:05:03.091][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:03.092][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:03.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.095][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.098][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.099][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.100][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.102][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.102][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:03.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.118][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-16 22:05:03.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:03.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.136][private$selectFields]
biodb.TRACE[2024-09-16 22:05:03.140][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:03.141][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:03.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.144][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.145][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.148][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.150][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.150][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.151][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.152][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.153][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.162][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:03.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:03.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.176][private$selectFields]
biodb.TRACE[2024-09-16 22:05:03.177][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:03.177][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:03.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.179][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.181][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.181][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.183][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.184][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.185][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:03.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.187][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.188][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:03.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:03.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.197][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-16 22:05:03.198][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:03.198][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:03.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:03.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:03.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:03.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:03.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:03.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:03.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:03.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:03.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:03.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:03.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:03.269][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:03.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:03.273][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:03.274][private$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[2024-09-16 22:05:03.676][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[2024-09-16 22:05:04.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:04.096][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-09-16 22:05:04.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-09-16 22:05:04.101][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[2024-09-16 22:05:04.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:04.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:04.105][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:05:04.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:05.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:05.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-09-16 22:05:05.222][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-09-16 22:05:05.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.290][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:05.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.335][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.335][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.336][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.338][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.339][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.342][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.343][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.345][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.346][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.347][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.356][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-16 22:05:05.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.392][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.393][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.394][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.394][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.395][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.396][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.397][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.398][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.401][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.409][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.411][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.412][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:05.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.442][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.442][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.443][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.444][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.447][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.450][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.450][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.451][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.454][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.454][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.463][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-16 22:05:05.464][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:05.465][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:05.470][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:05.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:05:05.475][biodb::testThat]
biodb.INFO [2024-09-16 22:05:05.476][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-09-16 22:05:05.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:05.478][biodb::testThat]
biodb.TRACE[2024-09-16 22:05:05.480][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-16 22:05:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-16 22:05:05.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:05.504][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.506][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-16 22:05:05.508][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.509][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-16 22:05:05.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.527][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.529][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-16 22:05:05.530][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.531][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-16 22:05:05.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.570][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:05.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.585][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.585][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.586][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.587][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.588][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.589][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.591][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.592][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.593][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.593][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.594][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.595][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.596][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.597][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.606][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-16 22:05:05.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.620][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.620][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.621][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.622][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.622][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.623][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.624][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.625][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.626][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.627][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.628][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.628][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.629][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.630][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.631][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.632][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:05.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.654][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.655][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.656][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.656][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.657][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.658][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.658][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.660][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.662][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.664][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.664][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.672][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.673][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.683][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-16 22:05:05.683][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:05.684][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:05.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:05.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.714][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-16 22:05:05.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-16 22:05:05.719][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.721][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-16 22:05:05.723][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.723][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-16 22:05:05.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:05.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.771][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:05.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.785][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.785][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.786][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.787][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.787][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.790][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.796][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.797][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.799][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.800][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.801][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.802][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.803][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.804][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.814][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-16 22:05:05.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.827][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.828][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.828][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.829][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.830][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.832][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.835][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.836][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.836][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.838][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.839][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.840][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.849][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:05.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.863][private$selectFields]
biodb.TRACE[2024-09-16 22:05:05.864][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:05.864][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:05.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.866][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.868][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.868][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.870][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.871][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.872][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:05.872][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.873][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.874][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.875][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:05.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:05.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.884][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-16 22:05:05.885][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:05.885][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:05.891][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:05.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:05.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:05:05.896][biodb::testThat]
biodb.INFO [2024-09-16 22:05:05.897][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-09-16 22:05:05.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:05.898][biodb::testThat]
biodb.TRACE[2024-09-16 22:05:05.900][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-16 22:05:05.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-16 22:05:05.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:05.932][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.934][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-09-16 22:05:05.936][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.937][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-09-16 22:05:05.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.954][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:05.956][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:05.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-09-16 22:05:05.958][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:05.959][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-09-16 22:05:05.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:05.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:05.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:05.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:05.991][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:05.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:05.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:05.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:05.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:05.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:05.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:05.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.005][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.005][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.006][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.007][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.007][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.008][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.009][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.010][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.011][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.013][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.014][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.017][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.018][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.027][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-09-16 22:05:06.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.046][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.047][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.048][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.051][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.052][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.053][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.054][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.055][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.058][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.059][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:06.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.081][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.082][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.082][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.083][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.086][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.089][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.090][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.090][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.093][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.094][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.103][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-09-16 22:05:06.103][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:06.104][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:06.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:06.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:06.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:06.376][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:06.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-09-16 22:05:06.378][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:06.379][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-09-16 22:05:06.382][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:06.385][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:06.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-09-16 22:05:06.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:06.388][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-09-16 22:05:06.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:06.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:06.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:06.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:06.447][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-09-16 22:05:06.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.462][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.463][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.463][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.464][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.465][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.465][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.467][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.468][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.470][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.471][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.472][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.474][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.474][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.484][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-09-16 22:05:06.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.491][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.TRACE[2024-09-16 22:05:06.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.497][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.498][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.499][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.499][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.503][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.505][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.507][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.509][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.510][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.519][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-09-16 22:05:06.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:06.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.539][private$selectFields]
biodb.TRACE[2024-09-16 22:05:06.540][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-09-16 22:05:06.540][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-09-16 22:05:06.541][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.542][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.544][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.545][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.547][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.547][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.548][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-09-16 22:05:06.549][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.549][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.551][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.551][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-09-16 22:05:06.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:06.560][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-09-16 22:05:06.561][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-09-16 22:05:06.562][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-09-16 22:05:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:06.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-09-16 22:05:06.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:06.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-16 22:05:06.579][biodb::testThat]
biodb.INFO [2024-09-16 22:05:06.580][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-09-16 22:05:06.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:06.581][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:06.582][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-09-16 22:05:06.583][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:05:06.584][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-09-16 22:05:06.585][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:05:06.586][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:05:06.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:05:06.587][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:06.588][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:05:06.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:05:06.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:06.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:06.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:06.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:06.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:06.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:06.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:06.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-09-16 22:05:06.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:06.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:06.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-09-16 22:05:07.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-09-16 22:05:07.430][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:07.432][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-09-16 22:05:07.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-09-16 22:05:07.436][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-09-16 22:05:07.437][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:05:07.438][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:05:07.439][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:05:07.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:07.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:07.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:07.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:07.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:07.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:07.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:07.449][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.451][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.454][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:07.455][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:07.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.457][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.457][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:07.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:07.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.459][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.460][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:07.461][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:07.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.462][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.463][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:07.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:07.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.465][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.466][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:07.467][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:07.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.469][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:07.470][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:07.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.471][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:07.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:07.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.474][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.483][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:07.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:07.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.486][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.487][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:07.488][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:07.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.489][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.490][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:07.491][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:07.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.492][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:07.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:07.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:07.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:07.521][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-09-16 22:05:07.522][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-09-16 22:05:07.527][biodb::testThat]
biodb.INFO [2024-09-16 22:05:07.528][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-09-16 22:05:07.529][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:07.529][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:07.538][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-09-16 22:05:07.538][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-09-16 22:05:07.539][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-09-16 22:05:07.540][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-09-16 22:05:07.541][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-09-16 22:05:07.542][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:05:07.543][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:05:07.544][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:07.544][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:05:07.545][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:05:07.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:07.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:07.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:07.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:07.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:07.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:07.555][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[2024-09-16 22:05:07.556][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-09-16 22:05:07.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:07.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:07.559][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-09-16 22:05:08.011][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-09-16 22:05:08.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:08.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-09-16 22:05:08.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-09-16 22:05:08.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:08.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:08.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:08.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:08.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:08.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:08.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:08.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-09-16 22:05:08.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:08.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:08.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-09-16 22:05:08.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-09-16 22:05:09.347][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:09.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-09-16 22:05:09.355][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-09-16 22:05:09.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:09.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:09.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:09.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:09.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:09.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:09.366][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[2024-09-16 22:05:09.367][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-09-16 22:05:09.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:09.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:09.370][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-09-16 22:05:09.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-09-16 22:05:10.211][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:10.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-09-16 22:05:10.216][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-09-16 22:05:10.218][private$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[2024-09-16 22:05:10.219][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:05:10.220][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-09-16 22:05:10.234][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-09-16 22:05:10.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:10.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:10.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:10.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:10.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:10.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:10.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:10.245][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.248][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.252][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:10.252][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:10.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.254][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.255][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:10.255][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:10.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.257][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:10.258][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:10.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.260][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.261][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.261][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.263][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.263][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.264][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.265][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.266][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:10.267][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:10.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.268][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.269][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.270][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.271][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.272][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:10.273][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:10.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.274][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.275][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:10.276][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:10.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.277][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:10.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:10.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.280][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:10.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:10.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:10.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:10.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:10.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:10.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:10.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:10.308][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.310][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.314][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:10.315][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:10.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.316][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.317][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:10.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:10.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.320][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:10.321][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:10.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.322][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:10.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.326][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:10.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:10.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.328][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:10.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.335][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.336][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.337][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.341][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.341][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.343][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.343][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.346][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:10.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:10.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.348][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:10.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:10.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.352][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.354][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:10.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:10.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.366][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:10.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:10.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.370][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:10.371][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:10.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.372][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:10.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:10.377][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:10.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.378][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:10.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:10.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:10.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:10.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:10.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:10.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:10.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:10.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:10.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:10.409][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.410][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.411][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.415][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:10.416][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:10.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.417][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.418][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:10.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:10.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.421][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:10.421][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:10.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.423][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:10.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:10.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:10.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.428][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:10.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:10.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.432][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.433][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.434][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.438][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.440][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.441][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:10.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.443][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:10.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:10.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.445][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.446][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:10.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:10.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.449][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.450][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.451][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.455][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:10.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:10.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.457][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:10.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:10.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.461][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:10.461][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:10.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.463][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.464][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:10.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:10.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:10.467][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:10.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:10.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:10.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:10.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:10.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:10.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:10.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:10.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:10.523][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-09-16 22:05:10.524][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-09-16 22:05:10.524][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-09-16 22:05:10.533][biodb::testThat]
biodb.INFO [2024-09-16 22:05:10.534][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-09-16 22:05:10.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:10.535][biodb::testThat]
biodb.INFO [2024-09-16 22:05:10.552][biodb::testThat]
biodb.INFO [2024-09-16 22:05:10.553][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-09-16 22:05:10.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:10.554][biodb::testThat]
biodb.INFO [2024-09-16 22:05:10.559][biodb::testThat]
biodb.INFO [2024-09-16 22:05:10.560][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-09-16 22:05:10.561][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:10.562][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:10.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:10.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:10.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:10.568][private$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[2024-09-16 22:05:11.078][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[2024-09-16 22:05:11.641][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:11.643][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-09-16 22:05:11.646][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-09-16 22:05:11.654][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:11.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:11.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:11.656][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:11.657][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:11.658][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:11.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:11.659][ef$get] fields variable is a list.
biodb.INFO [2024-09-16 22:05:11.660][biodb::testThat]
biodb.INFO [2024-09-16 22:05:11.661][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-09-16 22:05:11.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:11.662][biodb::testThat]
biodb.ERROR[2024-09-16 22:05:11.679][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-09-16 22:05:11.692][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-09-16 22:05:11.704][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-16 22:05:11.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-16 22:05:11.706][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-16 22:05:11.706][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-16 22:05:11.707][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:11.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:11.708][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.709][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-16 22:05:11.717][biodb::testContext]
biodb.INFO [2024-09-16 22:05:11.718][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:11.718][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-09-16 22:05:11.719][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:11.720][biodb::testContext]
biodb.INFO [2024-09-16 22:05:11.721][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:11.722][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:11.725][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:11.726][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-16 22:05:11.726][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.729][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-16 22:05:11.730][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.732][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-16 22:05:11.733][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.735][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-16 22:05:11.736][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-16 22:05:11.736][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-16 22:05:11.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.739][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-16 22:05:11.740][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-16 22:05:11.740][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.743][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-16 22:05:11.743][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-16 22:05:11.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.746][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-16 22:05:11.747][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-16 22:05:11.747][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-16 22:05:11.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.750][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-16 22:05:11.750][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.753][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-16 22:05:11.754][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-16 22:05:11.754][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-16 22:05:11.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.757][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:11.758][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-16 22:05:11.758][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-16 22:05:11.759][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-16 22:05:11.760][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-16 22:05:11.760][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-16 22:05:11.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.763][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-16 22:05:11.763][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-16 22:05:11.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.766][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-16 22:05:11.767][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-16 22:05:11.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.769][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-16 22:05:11.770][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-16 22:05:11.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.772][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-16 22:05:11.773][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-16 22:05:11.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.776][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-16 22:05:11.777][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-16 22:05:11.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.779][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:11.780][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-16 22:05:11.784][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-16 22:05:11.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.786][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-16 22:05:11.787][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-16 22:05:11.788][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-16 22:05:11.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.790][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-16 22:05:11.792][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.792][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-16 22:05:11.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.794][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:11.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.796][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.797][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:11.803][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:11.804][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.805][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-16 22:05:11.806][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:11.807][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:11.809][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:11.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:11.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.814][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.815][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:11.815][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:11.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.817][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.817][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-16 22:05:11.819][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.819][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:11.820][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.821][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:11.821][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.822][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.823][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.824][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:11.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:11.825][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.826][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-16 22:05:11.827][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:11.827][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.828][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.829][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:11.829][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:11.829][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:11.829][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:11.829][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:11.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:11.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.831][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:11.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.833][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.834][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.835][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:11.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:11.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.837][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.837][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-16 22:05:11.838][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.839][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-16 22:05:11.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.841][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:11.841][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.842][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.844][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:11.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:11.845][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.846][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-16 22:05:11.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:11.847][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.849][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:11.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:11.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.854][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:11.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:11.855][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.856][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.857][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-16 22:05:11.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.859][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:11.859][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:11.861][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.861][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.862][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.863][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:11.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:11.865][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.865][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-16 22:05:11.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:11.867][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:11.868][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.869][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:11.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.871][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:11.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:11.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:11.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:11.873][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:11.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:11.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:11.876][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:11.877][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:11.877][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.878][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[2024-09-16 22:05:11.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.893][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[2024-09-16 22:05:11.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.899][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[2024-09-16 22:05:11.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:11.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:11.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:11.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:11.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:11.911][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[2024-09-16 22:05:12.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.096][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-16 22:05:12.097][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-16 22:05:12.098][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-16 22:05:12.099][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-16 22:05:12.100][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:12.101][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-16 22:05:12.101][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:12.102][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:12.103][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-16 22:05:12.104][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-16 22:05:12.105][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:12.106][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-16 22:05:12.107][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:12.108][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:12.109][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-16 22:05:12.110][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-16 22:05:12.110][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-16 22:05:12.111][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-16 22:05:12.112][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:12.113][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-16 22:05:12.114][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-16 22:05:12.115][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-16 22:05:12.116][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-16 22:05:12.117][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-16 22:05:12.118][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-16 22:05:12.119][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-16 22:05:12.120][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-16 22:05:12.121][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-16 22:05:12.122][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-16 22:05:12.123][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-16 22:05:12.123][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-16 22:05:12.124][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-16 22:05:12.125][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-16 22:05:12.126][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-16 22:05:12.127][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-16 22:05:12.128][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-16 22:05:12.129][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-16 22:05:12.130][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-16 22:05:12.131][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-16 22:05:12.132][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-16 22:05:12.133][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-16 22:05:12.134][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-16 22:05:12.135][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-16 22:05:12.136][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-16 22:05:12.137][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-16 22:05:12.137][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-16 22:05:12.138][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-16 22:05:12.139][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-16 22:05:12.140][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-16 22:05:12.141][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-16 22:05:12.142][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-16 22:05:12.143][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-16 22:05:12.144][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-16 22:05:12.145][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-16 22:05:12.146][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-16 22:05:12.147][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-16 22:05:12.147][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-16 22:05:12.148][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-16 22:05:12.149][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-16 22:05:12.150][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-16 22:05:12.151][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-16 22:05:12.152][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-16 22:05:12.153][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-16 22:05:12.154][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-16 22:05:12.155][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-16 22:05:12.156][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-16 22:05:12.157][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:12.158][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:12.158][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-16 22:05:12.159][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-16 22:05:12.160][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-16 22:05:12.161][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-16 22:05:12.162][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-16 22:05:12.163][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-16 22:05:12.164][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-16 22:05:12.165][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-16 22:05:12.166][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-16 22:05:12.167][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-16 22:05:12.168][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-16 22:05:12.169][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-16 22:05:12.170][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-16 22:05:12.171][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-16 22:05:12.172][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-16 22:05:12.173][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-16 22:05:12.174][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:12.175][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:12.176][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.177][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.177][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[2024-09-16 22:05:12.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.202][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[2024-09-16 22:05:12.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.210][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.DEBUG[2024-09-16 22:05:12.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.214][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[2024-09-16 22:05:12.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.226][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[2024-09-16 22:05:12.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.238][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[2024-09-16 22:05:12.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:12.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:12.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:12.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:12.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:12.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:12.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:12.251][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:12.252][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-16 22:05:12.253][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:12.254][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-16 22:05:12.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:12.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:12.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:12.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:12.257][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:12.258][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-16 22:05:12.259][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-16 22:05:12.259][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:12.260][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:12.260][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-16 22:05:12.261][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-16 22:05:12.262][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-16 22:05:12.263][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:12.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:12.263][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:12.263][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:12.264][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-16 22:05:12.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:12.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:12.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:12.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:12.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:12.267][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:12.268][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:12.268][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-16 22:05:12.269][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:12.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:12.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:12.271][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-16 22:05:12.271][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-16 22:05:12.272][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:12.273][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:12.274][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-16 22:05:12.275][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:12.277][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:12.278][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:12.280][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-16 22:05:12.281][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-16 22:05:12.282][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-16 22:05:12.283][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-16 22:05:12.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:12.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:12.285][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-16 22:05:12.286][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-16 22:05:12.287][biodb::testThat]
biodb.INFO [2024-09-16 22:05:12.287][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-09-16 22:05:12.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:12.289][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:12.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-16 22:05:12.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:12.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:12.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-09-16 22:05:12.741][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-09-16 22:05:13.389][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:13.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-09-16 22:05:13.394][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-09-16 22:05:13.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:13.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:13.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:13.408][private$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[2024-09-16 22:05:14.129][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[2024-09-16 22:05:14.775][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:14.776][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-09-16 22:05:14.779][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-09-16 22:05:14.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:14.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:14.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:14.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:14.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:14.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:14.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:14.789][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[2024-09-16 22:05:14.791][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:14.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:14.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:05:15.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:15.681][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:15.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-09-16 22:05:15.685][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-09-16 22:05:15.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.712][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:15.715][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:15.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-16 22:05:15.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:15.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-16 22:05:15.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.725][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:15.727][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:15.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-16 22:05:15.729][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:15.730][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-16 22:05:15.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.746][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:15.748][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:15.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-09-16 22:05:15.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:15.751][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-09-16 22:05:15.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:15.761][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:15.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-09-16 22:05:15.763][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:15.764][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-09-16 22:05:15.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:15.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:15.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:15.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:15.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:15.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:15.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:15.781][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:15.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:15.784][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:15.785][private$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[2024-09-16 22:05:16.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:16.653][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:16.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-09-16 22:05:16.657][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-09-16 22:05:16.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:16.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:16.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:16.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:16.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:16.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:16.664][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.INFO [2024-09-16 22:05:16.668][biodb::testThat]
biodb.INFO [2024-09-16 22:05:16.669][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-09-16 22:05:16.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:16.670][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:16.672][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[2024-09-16 22:05:16.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:16.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:16.677][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:05:17.164][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:17.591][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:17.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-09-16 22:05:17.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-09-16 22:05:17.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:17.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:17.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:17.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:17.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:17.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:17.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:17.605][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:17.607][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:17.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:17.609][private$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[2024-09-16 22:05:18.065][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[2024-09-16 22:05:18.481][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:18.483][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-09-16 22:05:18.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-09-16 22:05:18.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:18.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.494][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.INFO [2024-09-16 22:05:18.498][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-16 22:05:18.499][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-16 22:05:18.499][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-16 22:05:18.500][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-16 22:05:18.500][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.502][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.503][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-16 22:05:18.506][biodb::testContext]
biodb.INFO [2024-09-16 22:05:18.506][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:18.507][biodb::testContext] Test context - Test web services
biodb.INFO [2024-09-16 22:05:18.508][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:18.508][biodb::testContext]
biodb.INFO [2024-09-16 22:05:18.510][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:18.511][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:18.514][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:18.514][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-16 22:05:18.515][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.518][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-16 22:05:18.519][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.521][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-16 22:05:18.522][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.525][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-16 22:05:18.525][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-16 22:05:18.526][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-16 22:05:18.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.528][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-16 22:05:18.529][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-16 22:05:18.530][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.532][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-16 22:05:18.533][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-16 22:05:18.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.535][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-16 22:05:18.536][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-16 22:05:18.537][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-16 22:05:18.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.539][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-16 22:05:18.540][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.542][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[2024-09-16 22:05:18.542][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-16 22:05:18.543][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-16 22:05:18.544][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-16 22:05:18.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.558][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:18.559][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-16 22:05:18.560][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-16 22:05:18.560][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-16 22:05:18.561][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-16 22:05:18.562][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-16 22:05:18.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.564][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-16 22:05:18.565][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-16 22:05:18.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.567][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-16 22:05:18.568][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-16 22:05:18.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.570][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-16 22:05:18.571][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-16 22:05:18.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.573][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-16 22:05:18.574][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-16 22:05:18.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.576][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-16 22:05:18.577][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-16 22:05:18.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.579][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:18.580][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-16 22:05:18.583][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-16 22:05:18.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.585][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-16 22:05:18.586][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-16 22:05:18.587][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-16 22:05:18.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.589][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-16 22:05:18.591][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.591][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-16 22:05:18.592][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.593][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:18.593][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.595][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.596][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:18.597][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:18.597][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.598][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-16 22:05:18.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:18.599][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.600][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:18.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:18.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:18.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.605][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.606][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:18.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:18.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.608][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.609][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-16 22:05:18.610][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.611][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:18.612][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:18.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.615][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:18.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:18.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.617][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-16 22:05:18.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:18.619][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.619][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.620][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:18.620][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:18.620][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:18.620][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:18.620][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:18.621][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:18.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.623][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:18.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.624][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.625][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.626][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:18.626][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:18.627][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.628][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.628][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-16 22:05:18.629][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.630][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-16 22:05:18.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:18.632][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.633][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.633][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.634][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.635][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:18.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:18.636][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.637][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-16 22:05:18.637][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:18.638][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.639][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.640][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:18.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.642][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:18.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.645][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.645][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:18.646][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:18.646][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.647][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.648][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-16 22:05:18.649][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.650][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:18.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:18.652][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.655][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:18.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:18.656][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.657][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-16 22:05:18.657][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:18.658][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.659][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.660][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:18.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:18.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.664][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.665][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:18.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:18.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.667][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:18.668][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:18.673][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.676][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[2024-09-16 22:05:18.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.682][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[2024-09-16 22:05:18.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.685][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[2024-09-16 22:05:18.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.688][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[2024-09-16 22:05:18.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.694][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[2024-09-16 22:05:18.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.725][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[2024-09-16 22:05:18.726][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-16 22:05:18.727][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-16 22:05:18.728][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-16 22:05:18.729][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-16 22:05:18.730][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:18.731][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-16 22:05:18.732][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:18.733][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:18.734][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-16 22:05:18.735][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-16 22:05:18.736][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:18.737][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-16 22:05:18.738][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:18.738][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:18.739][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-16 22:05:18.740][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-16 22:05:18.741][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-16 22:05:18.742][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-16 22:05:18.743][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:18.744][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-16 22:05:18.745][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-16 22:05:18.746][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-16 22:05:18.747][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-16 22:05:18.748][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-16 22:05:18.749][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-16 22:05:18.750][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-16 22:05:18.751][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-16 22:05:18.752][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-16 22:05:18.753][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-16 22:05:18.754][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-16 22:05:18.755][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-16 22:05:18.755][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-16 22:05:18.756][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-16 22:05:18.757][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-16 22:05:18.758][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-16 22:05:18.759][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-16 22:05:18.760][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-16 22:05:18.761][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-16 22:05:18.762][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-16 22:05:18.763][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-16 22:05:18.764][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-16 22:05:18.765][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-16 22:05:18.766][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-16 22:05:18.767][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-16 22:05:18.768][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-16 22:05:18.769][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-16 22:05:18.770][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-16 22:05:18.771][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-16 22:05:18.772][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-16 22:05:18.773][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-16 22:05:18.774][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-16 22:05:18.775][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-16 22:05:18.776][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-16 22:05:18.777][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-16 22:05:18.778][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-16 22:05:18.779][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-16 22:05:18.780][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-16 22:05:18.781][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-16 22:05:18.782][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-16 22:05:18.783][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-16 22:05:18.788][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-16 22:05:18.789][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-16 22:05:18.790][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-16 22:05:18.791][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-16 22:05:18.792][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-16 22:05:18.793][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-16 22:05:18.794][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:18.795][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:18.796][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-16 22:05:18.797][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-16 22:05:18.798][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-16 22:05:18.799][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-16 22:05:18.800][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-16 22:05:18.801][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-16 22:05:18.802][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-16 22:05:18.803][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-16 22:05:18.804][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-16 22:05:18.805][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-16 22:05:18.806][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-16 22:05:18.807][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-16 22:05:18.808][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-16 22:05:18.809][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-16 22:05:18.810][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-16 22:05:18.812][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-16 22:05:18.813][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:18.814][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:18.815][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.816][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.822][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[2024-09-16 22:05:18.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.836][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[2024-09-16 22:05:18.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.852][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.DEBUG[2024-09-16 22:05:18.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.856][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[2024-09-16 22:05:18.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.864][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[2024-09-16 22:05:18.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.872][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[2024-09-16 22:05:18.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:18.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:18.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:18.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:18.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:18.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:18.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:18.890][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:18.891][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-16 22:05:18.892][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.893][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.894][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.894][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:18.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.896][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.897][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-16 22:05:18.898][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-16 22:05:18.898][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:18.899][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.900][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-16 22:05:18.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-16 22:05:18.906][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:18.907][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:18.907][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:18.907][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:18.908][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-16 22:05:18.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.909][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:18.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:18.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:18.911][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:18.912][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:18.912][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-16 22:05:18.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:18.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:18.914][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:18.914][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-16 22:05:18.914][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-16 22:05:18.915][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:18.917][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:18.918][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-16 22:05:18.918][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:18.920][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:18.921][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:18.923][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-16 22:05:18.924][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-16 22:05:18.924][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-16 22:05:18.925][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-16 22:05:18.926][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:18.927][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:18.928][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-16 22:05:18.928][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-16 22:05:18.929][biodb::testThat]
biodb.INFO [2024-09-16 22:05:18.930][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-09-16 22:05:18.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:18.931][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:18.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-16 22:05:18.936][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:18.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-16 22:05:18.938][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:18.939][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-16 22:05:18.942][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[2024-09-16 22:05:18.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:18.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:18.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-09-16 22:05:19.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-09-16 22:05:19.864][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:19.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-09-16 22:05:19.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-09-16 22:05:19.883][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-16 22:05:19.884][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-16 22:05:19.885][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-16 22:05:19.885][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-16 22:05:19.886][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:19.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:19.887][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:19.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:19.888][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-16 22:05:19.891][biodb::testContext]
biodb.INFO [2024-09-16 22:05:19.892][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:19.893][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-09-16 22:05:19.893][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-16 22:05:19.894][biodb::testContext]
biodb.INFO [2024-09-16 22:05:19.895][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:19.897][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:19.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:19.900][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-16 22:05:19.901][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.903][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-16 22:05:19.904][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.906][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-16 22:05:19.907][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.909][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-16 22:05:19.910][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-16 22:05:19.911][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-16 22:05:19.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.913][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-16 22:05:19.914][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-16 22:05:19.914][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.916][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.DEBUG[2024-09-16 22:05:19.917][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-16 22:05:19.917][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-16 22:05:19.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.920][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-16 22:05:19.920][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-16 22:05:19.921][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-16 22:05:19.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.923][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[2024-09-16 22:05:19.924][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-16 22:05:19.924][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.927][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-16 22:05:19.928][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-16 22:05:19.928][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-16 22:05:19.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.931][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:19.931][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-16 22:05:19.932][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-16 22:05:19.933][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-16 22:05:19.933][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-16 22:05:19.934][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-16 22:05:19.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.936][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-16 22:05:19.937][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-16 22:05:19.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.940][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-16 22:05:19.940][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-16 22:05:19.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.943][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-16 22:05:19.943][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-16 22:05:19.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.952][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[2024-09-16 22:05:19.953][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-16 22:05:19.954][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-16 22:05:19.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.956][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-16 22:05:19.957][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-16 22:05:19.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.959][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[2024-09-16 22:05:19.959][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-16 22:05:19.960][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-16 22:05:19.964][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-16 22:05:19.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.966][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-16 22:05:19.967][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-16 22:05:19.967][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-16 22:05:19.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:19.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:19.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:19.970][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-16 22:05:19.971][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:19.972][self$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[2024-09-16 22:05:19.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:19.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.975][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:19.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:19.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:19.977][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:19.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:19.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.979][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-16 22:05:19.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:19.980][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:19.980][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.981][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:19.981][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:19.981][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:19.981][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:19.981][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:19.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:19.982][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:19.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:19.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:19.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:19.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:19.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:19.986][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:19.987][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:19.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:19.988][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:19.988][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:19.989][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-16 22:05:19.990][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:19.991][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:19.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.992][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:19.993][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:19.994][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:19.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:19.996][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:19.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:19.997][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:19.998][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-16 22:05:19.998][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:19.999][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:19.999][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.000][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:20.000][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:20.000][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:20.000][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-16 22:05:20.000][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-16 22:05:20.001][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:20.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:20.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.005][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:20.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:20.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.008][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.008][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-16 22:05:20.009][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.010][self$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[2024-09-16 22:05:20.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:20.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.013][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.014][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.015][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-16 22:05:20.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:20.016][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.017][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-16 22:05:20.017][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:20.018][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.019][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.019][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.020][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:20.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.022][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:20.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.024][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:20.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:20.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.027][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.027][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-16 22:05:20.029][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.029][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-16 22:05:20.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:20.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.034][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-16 22:05:20.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:20.035][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.036][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-16 22:05:20.036][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:20.037][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.038][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-16 22:05:20.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.041][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:20.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.043][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.044][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:20.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:20.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.046][self$setPropertyValue]
biodb.DEBUG[2024-09-16 22:05:20.047][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:20.048][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.057][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[2024-09-16 22:05:20.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.076][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[2024-09-16 22:05:20.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.082][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.DEBUG[2024-09-16 22:05:20.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.099][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[2024-09-16 22:05:20.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.102][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-16 22:05:20.103][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-16 22:05:20.104][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-16 22:05:20.105][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-16 22:05:20.106][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:20.107][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-16 22:05:20.108][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:20.109][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:20.110][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-16 22:05:20.111][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-16 22:05:20.112][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:20.113][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-16 22:05:20.113][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-16 22:05:20.114][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-16 22:05:20.115][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-16 22:05:20.116][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-16 22:05:20.117][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-16 22:05:20.118][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-16 22:05:20.119][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:20.120][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-16 22:05:20.121][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-16 22:05:20.122][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-16 22:05:20.123][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-16 22:05:20.123][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-16 22:05:20.124][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-16 22:05:20.125][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-16 22:05:20.126][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-16 22:05:20.127][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-16 22:05:20.128][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-16 22:05:20.129][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-16 22:05:20.130][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-16 22:05:20.131][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-16 22:05:20.132][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-16 22:05:20.132][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-16 22:05:20.133][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-16 22:05:20.134][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-16 22:05:20.135][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-16 22:05:20.136][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-16 22:05:20.137][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-16 22:05:20.138][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-16 22:05:20.139][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-16 22:05:20.140][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-16 22:05:20.141][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-16 22:05:20.142][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-16 22:05:20.143][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-16 22:05:20.143][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-16 22:05:20.144][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-16 22:05:20.145][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-16 22:05:20.146][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-16 22:05:20.147][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-16 22:05:20.148][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-16 22:05:20.149][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-16 22:05:20.150][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-16 22:05:20.151][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-16 22:05:20.152][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-16 22:05:20.153][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-16 22:05:20.154][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-16 22:05:20.155][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-16 22:05:20.156][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-16 22:05:20.157][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-16 22:05:20.158][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-16 22:05:20.158][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-16 22:05:20.159][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-16 22:05:20.160][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-16 22:05:20.161][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-16 22:05:20.162][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-16 22:05:20.163][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:20.164][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:20.165][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-16 22:05:20.166][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-16 22:05:20.167][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-16 22:05:20.168][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-16 22:05:20.172][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-16 22:05:20.173][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-16 22:05:20.174][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-16 22:05:20.175][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-16 22:05:20.176][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-16 22:05:20.177][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-16 22:05:20.178][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-16 22:05:20.179][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-16 22:05:20.180][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-16 22:05:20.181][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-16 22:05:20.182][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-16 22:05:20.183][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-16 22:05:20.184][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-16 22:05:20.185][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-16 22:05:20.185][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.186][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.227][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[2024-09-16 22:05:20.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.235][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[2024-09-16 22:05:20.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-16 22:05:20.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.256][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-09-16 22:05:20.257][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-09-16 22:05:20.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.259][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.260][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.261][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-16 22:05:20.262][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.262][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.263][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.264][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-09-16 22:05:20.264][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-16 22:05:20.265][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-16 22:05:20.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.266][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-09-16 22:05:20.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-09-16 22:05:20.268][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-16 22:05:20.269][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-16 22:05:20.269][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-16 22:05:20.269][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-16 22:05:20.270][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-16 22:05:20.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-16 22:05:20.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-16 22:05:20.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-16 22:05:20.274][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-16 22:05:20.275][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:20.275][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-09-16 22:05:20.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-16 22:05:20.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-16 22:05:20.281][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-16 22:05:20.282][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-09-16 22:05:20.282][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-09-16 22:05:20.283][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-16 22:05:20.284][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-16 22:05:20.285][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-09-16 22:05:20.286][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-16 22:05:20.287][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-16 22:05:20.288][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-16 22:05:20.290][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-09-16 22:05:20.291][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-09-16 22:05:20.292][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-09-16 22:05:20.293][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-09-16 22:05:20.294][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:20.294][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-16 22:05:20.295][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-09-16 22:05:20.296][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-09-16 22:05:20.297][biodb::testThat]
biodb.INFO [2024-09-16 22:05:20.297][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-09-16 22:05:20.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-16 22:05:20.299][biodb::testThat]
biodb.DEBUG[2024-09-16 22:05:20.301][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-09-16 22:05:20.303][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:20.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-09-16 22:05:20.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:20.306][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-09-16 22:05:20.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-09-16 22:05:20.311][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-16 22:05:20.311][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-09-16 22:05:20.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-16 22:05:20.313][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-09-16 22:05:20.316][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-09-16 22:05:20.317][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-09-16 22:05:20.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-09-16 22:05:20.319][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-09-16 22:05:20.319][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-16 22:05:20.320][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-09-16 22:05:20.321][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-09-16 22:05:20.321][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-16 22:05:20.322][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-16 22:05:20.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:20.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:20.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:20.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:20.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:20.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:20.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-16 22:05:20.331][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-09-16 22:05:20.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-16 22:05:20.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-16 22:05:20.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-09-16 22:05:20.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-09-16 22:05:21.673][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-16 22:05:21.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-09-16 22:05:21.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-09-16 22:05:21.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-09-16 22:05:21.682][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-16 22:05:21.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-09-16 22:05:21.683][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-09-16 22:05:21.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-16 22:05:21.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:21.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:21.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:21.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:21.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:21.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-16 22:05:21.694][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.696][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.700][ef$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:21.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:21.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.702][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-09-16 22:05:21.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-09-16 22:05:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.705][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:21.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:21.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.707][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-16 22:05:21.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-16 22:05:21.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.711][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-16 22:05:21.712][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-16 22:05:21.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.713][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.714][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-16 22:05:21.715][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-16 22:05:21.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.716][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:21.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:21.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.719][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.720][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-16 22:05:21.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.723][ef$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:21.724][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:21.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.725][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.726][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-09-16 22:05:21.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-09-16 22:05:21.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:21.729][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:21.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.731][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:21.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-16 22:05:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.734][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:21.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:21.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.736][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-16 22:05:21.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-16 22:05:21.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.747][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:21.748][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:21.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.749][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.750][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-09-16 22:05:21.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-09-16 22:05:21.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.753][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:21.754][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:21.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.755][ef$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-16 22:05:21.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-16 22:05:21.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-16 22:05:21.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-16 22:05:21.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-16 22:05:21.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-16 22:05:21.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-16 22:05:21.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-16 22:05:21.785][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-09-16 22:05:21.788][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-16 22:05:21.789][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-09-16 22:05:21.789][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-09-16 22:05:21.790][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-16 22:05:21.791][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-16 22:05:21.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-16 22:05:21.792][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-16 22:05:21.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-16 22:05:21.793][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-16 22:05:21.794][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
15.503 1.005 54.230
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.660 | 0.062 | 1.471 | |
| ChebiEntry | 0.105 | 0.002 | 0.107 | |