Pierrick Roger
| Snapshot Date: 2024-10-02 13:40 -0400 (Wed, 02 Oct 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 2024-10-03 11:39 -0400 (Thu, 03 Oct 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" | 4461 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 201/2266 | 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 | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| 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: 2024-10-02 21:40:48 -0400 (Wed, 02 Oct 2024) |
| EndedAt: 2024-10-02 21:42:36 -0400 (Wed, 02 Oct 2024) |
| EllapsedTime: 108.1 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 [2024-10-02 21:41:22.374][biodb::testContext]
biodb.INFO [2024-10-02 21:41:22.376][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:41:22.377][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-02 21:41:22.378][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:41:22.379][biodb::testContext]
biodb.INFO [2024-10-02 21:41:22.384][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:41:22.386][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 21:41:22.392][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:41:22.393][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 21:41:22.394][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.397][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 21:41:22.415][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.418][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[2024-10-02 21:41:22.419][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 21:41:22.419][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.423][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 21:41:22.424][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 21:41:22.425][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 21:41:22.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.427][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[2024-10-02 21:41:22.428][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 21:41:22.429][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 21:41:22.430][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.433][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 21:41:22.434][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 21:41:22.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.436][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[2024-10-02 21:41:22.437][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 21:41:22.438][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 21:41:22.439][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 21:41:22.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.442][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 21:41:22.443][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 21:41:22.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 21:41:22.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 21:41:22.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.452][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:41:22.452][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 21:41:22.453][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 21:41:22.454][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 21:41:22.455][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 21:41:22.456][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 21:41:22.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.459][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 21:41:22.460][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 21:41:22.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.463][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 21:41:22.464][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 21:41:22.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.468][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 21:41:22.469][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 21:41:22.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.472][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 21:41:22.473][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 21:41:22.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.476][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 21:41:22.477][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 21:41:22.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.480][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:41:22.481][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 21:41:22.485][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-10-02 21:41:22.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.488][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 21:41:22.489][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 21:41:22.490][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 21:41:22.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.496][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 21:41:22.528][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.550][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 21:41:22.551][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:41:22.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.555][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:41:22.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:41:22.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.557][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 21:41:22.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:41:22.558][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:41:22.559][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:41:22.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:41:22.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:41:22.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.565][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.565][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:41:22.566][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:41:22.566][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.567][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.568][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 21:41:22.569][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.570][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:41:22.571][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.571][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:41:22.572][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.573][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.573][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.574][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.575][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:41:22.575][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:41:22.576][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.577][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 21:41:22.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:41:22.578][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:41:22.579][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:41:22.580][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:41:22.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.582][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:41:22.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.584][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.585][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.585][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:41:22.586][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:41:22.586][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.587][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.588][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 21:41:22.589][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.590][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 21:41:22.590][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.591][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:41:22.592][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.592][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.593][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.594][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.594][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:41:22.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:41:22.596][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.596][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 21:41:22.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:41:22.598][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.599][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:41:22.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.602][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:41:22.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.604][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:41:22.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:41:22.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.607][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.607][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 21:41:22.609][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.609][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:41:22.610][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.611][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:41:22.611][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.612][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.613][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.613][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.614][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:41:22.615][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:41:22.615][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.616][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 21:41:22.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:41:22.617][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.618][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.619][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:41:22.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.620][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.621][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:41:22.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.623][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.624][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.624][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:41:22.625][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:41:22.625][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.626][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:41:22.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:41:22.629][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.630][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[2024-10-02 21:41:22.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.633][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.DEBUG[2024-10-02 21:41:22.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.648][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.DEBUG[2024-10-02 21:41:22.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.682][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[2024-10-02 21:41:22.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.688][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 21:41:22.693][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 21:41:22.695][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 21:41:22.696][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 21:41:22.698][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:41:22.699][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 21:41:22.701][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 21:41:22.702][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 21:41:22.704][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 21:41:22.705][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 21:41:22.707][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:41:22.708][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 21:41:22.710][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 21:41:22.711][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 21:41:22.713][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 21:41:22.714][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 21:41:22.716][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 21:41:22.717][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 21:41:22.719][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:41:22.720][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 21:41:22.722][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 21:41:22.723][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 21:41:22.725][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 21:41:22.726][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 21:41:22.728][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 21:41:22.729][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 21:41:22.731][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 21:41:22.732][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 21:41:22.733][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 21:41:22.735][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 21:41:22.736][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 21:41:22.738][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 21:41:22.739][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 21:41:22.741][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 21:41:22.742][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 21:41:22.744][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 21:41:22.745][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 21:41:22.747][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 21:41:22.748][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 21:41:22.750][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 21:41:22.751][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 21:41:22.772][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 21:41:22.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 21:41:22.774][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 21:41:22.775][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 21:41:22.776][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 21:41:22.777][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 21:41:22.778][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 21:41:22.779][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 21:41:22.780][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 21:41:22.781][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 21:41:22.782][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 21:41:22.783][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 21:41:22.784][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 21:41:22.784][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 21:41:22.786][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 21:41:22.787][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 21:41:22.787][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 21:41:22.788][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 21:41:22.789][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 21:41:22.790][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 21:41:22.791][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 21:41:22.792][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 21:41:22.793][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 21:41:22.794][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 21:41:22.795][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 21:41:22.796][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:41:22.797][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:41:22.798][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 21:41:22.799][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 21:41:22.800][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 21:41:22.801][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 21:41:22.802][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 21:41:22.803][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 21:41:22.804][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 21:41:22.804][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 21:41:22.805][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 21:41:22.806][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 21:41:22.807][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 21:41:22.808][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 21:41:22.809][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 21:41:22.810][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 21:41:22.811][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 21:41:22.815][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 21:41:22.816][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:41:22.819][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:41:22.819][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.820][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:22.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.832][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[2024-10-02 21:41:22.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.836][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[2024-10-02 21:41:22.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.840][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[2024-10-02 21:41:22.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.844][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[2024-10-02 21:41:22.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.848][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[2024-10-02 21:41:22.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.852][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[2024-10-02 21:41:22.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.856][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[2024-10-02 21:41:22.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.860][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[2024-10-02 21:41:22.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.864][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[2024-10-02 21:41:22.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.868][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[2024-10-02 21:41:22.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.872][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[2024-10-02 21:41:22.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.877][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[2024-10-02 21:41:22.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.881][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[2024-10-02 21:41:22.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.885][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[2024-10-02 21:41:22.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.889][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[2024-10-02 21:41:22.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:41:22.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.893][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[2024-10-02 21:41:22.894][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 21:41:22.901][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 21:41:22.903][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.903][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:41:22.905][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.906][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.907][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.907][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 21:41:22.908][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 21:41:22.909][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:41:22.909][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.910][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 21:41:22.911][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 21:41:22.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 21:41:22.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:41:22.913][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:41:22.913][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:41:22.913][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 21:41:22.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.915][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:41:22.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:41:22.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:41:22.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:41:22.918][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:22.918][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 21:41:22.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:41:22.919][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:41:22.920][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 21:41:22.920][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 21:41:22.920][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 21:41:22.924][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:41:22.926][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:41:22.927][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 21:41:22.928][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:41:22.929][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:41:22.930][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:41:22.950][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 21:41:22.951][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 21:41:22.953][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 21:41:22.956][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 21:41:22.958][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:41:22.959][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:41:22.960][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 21:41:22.961][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 21:41:22.967][biodb::testThat]
biodb.INFO [2024-10-02 21:41:22.967][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-10-02 21:41:22.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:22.969][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:22.972][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[2024-10-02 21:41:22.973][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:22.975][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:22.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:22.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:22.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:22.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:22.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:22.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:22.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:23.000][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.001][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.003][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.015][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.016][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.017][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.039][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.039][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.041][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.044][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.045][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.046][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.050][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.051][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.052][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.056][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.057][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.058][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.059][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.062][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:23.062][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.064][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.064][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:23.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.067][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.068][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.073][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.074][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.075][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.079][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:23.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.081][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:23.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.085][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.087][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.088][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:23.149][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-10-02 21:41:23.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:23.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:23.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:23.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:23.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:23.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:23.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:23.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:23.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.260][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.260][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.262][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.302][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.303][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.304][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.321][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.323][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.339][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.340][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.342][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.350][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.358][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.358][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.360][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.377][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.378][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.389][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.392][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.395][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.395][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.397][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.405][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.408][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.410][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.413][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.415][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.416][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.423][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.426][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.429][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.431][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.433][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.434][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.447][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.449][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.450][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.456][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.457][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.473][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.475][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.491][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.492][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.493][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.501][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.507][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.507][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.509][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.512][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.512][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.514][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.517][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.517][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.519][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.522][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.523][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.524][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.527][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.528][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.529][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.532][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.533][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.534][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.537][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.538][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.539][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.542][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.543][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.544][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.548][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.549][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.552][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.553][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.554][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:23.559][biodb::testThat]
biodb.INFO [2024-10-02 21:41:23.560][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-02 21:41:23.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:23.561][biodb::testThat]
biodb.DEBUG[2024-10-02 21:41:23.571][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-10-02 21:41:23.576][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:23.579][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-10-02 21:41:23.580][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:23.581][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-10-02 21:41:23.581][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:23.598][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:23.599][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:23.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:23.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:23.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:23.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:23.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:23.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:23.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:23.612][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.613][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.614][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.630][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.631][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.632][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.633][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:23.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:23.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.636][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.636][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.638][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:23.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:23.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:23.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.647][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.649][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:23.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.652][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.653][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.654][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.655][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:23.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.658][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:23.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.660][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.661][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:23.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:23.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.663][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.665][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:23.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.669][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.671][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.675][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:23.675][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.677][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.677][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:23.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:23.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.681][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.682][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.683][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:23.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:23.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:23.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:23.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:23.712][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-10-02 21:41:23.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-02 21:41:23.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-02 21:41:23.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-02 21:41:23.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-02 21:41:23.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-02 21:41:23.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-02 21:41:23.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:23.726][biodb::testThat]
biodb.INFO [2024-10-02 21:41:23.726][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-02 21:41:23.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:23.728][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:23.730][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.732][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:23.733][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-10-02 21:41:23.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:23.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:23.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:23.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:23.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:23.764][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-10-02 21:41:23.767][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 21:41:23.782][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:23.793][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 21:41:23.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:23.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 21:41:23.811][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[2024-10-02 21:41:23.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:23.814][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:23.815][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:41:24.435][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:41:24.974][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:24.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-02 21:41:25.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-02 21:41:25.002][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-10-02 21:41:25.011][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:25.012][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:25.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.013][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.014][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.015][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.016][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:25.019][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.019][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-10-02 21:41:25.020][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:25.021][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:25.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:25.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:25.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:25.085][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:25.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:25.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:25.089][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:25.090][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-10-02 21:41:25.101][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.102][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-10-02 21:41:25.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:25.103][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:25.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:25.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:25.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:25.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:25.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.138][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:25.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:25.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:25.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:25.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:25.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:25.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:25.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-02 21:41:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-02 21:41:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:25.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:25.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-02 21:41:25.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:25.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:25.194][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.194][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-02 21:41:25.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:25.196][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.201][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.202][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-02 21:41:25.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:25.203][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.209][biodb::testThat]
biodb.INFO [2024-10-02 21:41:25.210][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-02 21:41:25.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:25.211][biodb::testThat]
biodb.DEBUG[2024-10-02 21:41:25.213][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-10-02 21:41:25.895][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-10-02 21:41:26.909][biodb::testThat]
biodb.INFO [2024-10-02 21:41:26.910][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-02 21:41:26.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:26.911][biodb::testThat]
biodb.DEBUG[2024-10-02 21:41:27.360][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[2024-10-02 21:41:27.795][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:27.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:27.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.797][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.798][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:27.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:27.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.800][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:27.801][biodb::testThat]
biodb.INFO [2024-10-02 21:41:27.802][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-10-02 21:41:27.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:27.803][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:27.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:27.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:27.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:27.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:27.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:27.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:27.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:27.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:27.882][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:27.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:27.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:27.884][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 21:41:27.926][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:27.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:27.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:27.930][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:27.931][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-10-02 21:41:27.940][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 21:41:27.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 21:41:27.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:27.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:27.969][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:27.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:27.981][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:27.992][private$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[2024-10-02 21:41:28.394][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[2024-10-02 21:41:28.790][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:28.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-02 21:41:28.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-02 21:41:28.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:28.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:28.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:28.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:28.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:28.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:28.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:28.803][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-10-02 21:41:28.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:28.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-10-02 21:41:28.837][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:28.838][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:28.839][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:28.840][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:28.840][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:28.841][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:28.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:28.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:28.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:28.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:28.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:28.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:28.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:28.850][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-10-02 21:41:28.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:28.852][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:28.853][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-10-02 21:41:29.258][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-10-02 21:41:29.661][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:29.663][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-10-02 21:41:29.665][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-10-02 21:41:29.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-10-02 21:41:29.668][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:29.669][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:29.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:29.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:29.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:29.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:29.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:29.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:29.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:29.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:29.680][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.682][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.686][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:29.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:29.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.688][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.689][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:29.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.691][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:29.692][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:29.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.693][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:29.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:29.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:29.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:29.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.699][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:29.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.703][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:29.704][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:29.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.705][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:29.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.708][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:29.709][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:29.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.710][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.711][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:29.712][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.713][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.714][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:29.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:29.718][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:29.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.719][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:29.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.722][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:29.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:29.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.724][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:29.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:29.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.728][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:29.729][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:29.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.730][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:29.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:29.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.734][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:29.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:29.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.736][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:29.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:29.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:29.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:29.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:29.766][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-10-02 21:41:29.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:29.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:29.789][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[2024-10-02 21:41:29.792][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:29.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:29.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:41:30.194][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:41:30.593][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:30.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-02 21:41:30.597][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-02 21:41:30.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:30.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:30.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:30.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:30.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:30.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:30.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:30.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:30.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:30.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:30.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:30.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:30.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:30.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:30.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:30.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:30.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:30.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:30.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:30.631][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-10-02 21:41:30.632][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:30.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-10-02 21:41:30.634][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:30.635][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:30.635][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:30.636][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:30.637][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:30.637][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:30.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:30.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:30.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:30.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:30.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:30.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:30.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:30.654][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-10-02 21:41:30.656][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:30.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:30.657][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-10-02 21:41:31.083][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-10-02 21:41:31.480][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:31.481][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-10-02 21:41:31.483][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-10-02 21:41:31.485][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-10-02 21:41:31.486][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:31.487][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:31.488][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:31.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:31.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:31.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:31.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:31.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:31.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:31.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:31.497][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.497][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.499][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.502][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:31.503][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:31.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:31.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.508][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:31.508][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:31.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.510][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.511][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:31.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:31.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.513][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:31.514][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:31.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.515][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:31.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:31.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.519][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:31.519][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:31.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.521][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:31.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:31.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.534][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:31.535][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:31.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.536][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.537][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:31.537][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.539][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.540][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.542][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:31.543][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:31.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.544][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:31.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:31.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.548][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:31.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:31.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.550][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:31.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.554][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:31.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:31.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.556][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:31.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:31.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.559][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:31.560][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:31.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.562][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:31.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:31.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:31.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:31.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:31.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:31.591][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-10-02 21:41:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:31.612][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:31.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:31.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:31.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:31.617][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 21:41:31.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:31.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:31.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:31.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:31.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:31.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:31.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:31.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:31.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:31.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:31.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:31.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:31.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:31.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:31.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:31.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:31.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:31.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:31.641][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-10-02 21:41:31.642][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:31.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-10-02 21:41:31.644][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:31.644][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:31.645][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:31.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:31.647][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:31.647][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:31.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:31.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:31.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:31.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:31.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:31.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:31.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:31.660][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-10-02 21:41:31.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:31.663][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:31.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-10-02 21:41:32.065][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-10-02 21:41:32.466][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:32.468][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-10-02 21:41:32.471][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-10-02 21:41:32.473][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-10-02 21:41:32.474][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:32.475][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:32.475][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:32.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:32.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:32.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:32.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:32.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:32.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:32.483][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.TRACE[2024-10-02 21:41:32.485][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.486][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.487][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.491][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:32.491][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:32.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.493][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.494][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:32.494][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:32.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.496][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.497][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:32.497][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:32.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.499][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:32.500][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:32.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.501][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:32.503][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:32.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.505][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:32.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.507][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:32.508][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:32.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.510][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.511][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:32.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:32.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.513][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:32.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:32.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:32.517][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:32.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.518][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.519][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:32.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:32.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.522][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:32.522][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:32.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.524][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:32.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:32.551][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-10-02 21:41:32.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:32.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:32.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:32.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:32.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:32.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:32.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:32.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:32.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:32.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:32.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:32.573][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-10-02 21:41:32.574][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:32.575][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-10-02 21:41:32.576][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:32.577][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:32.578][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:32.578][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:32.584][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:32.587][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:32.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:32.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:32.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:32.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:32.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:32.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:32.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:32.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-10-02 21:41:32.599][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:32.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:32.601][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-10-02 21:41:32.998][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-10-02 21:41:33.400][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-02 21:41:33.402][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-02 21:41:33.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-10-02 21:41:33.406][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-10-02 21:41:33.408][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-10-02 21:41:33.409][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:33.410][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:33.411][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:33.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:33.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:33.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:33.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:33.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:33.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:33.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:33.421][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.423][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.426][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:33.427][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:33.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.428][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.429][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:33.430][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:33.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.431][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:33.433][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:33.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.434][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.435][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:33.436][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:33.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.437][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:33.438][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:33.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.440][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.440][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:33.441][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.443][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.443][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:33.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:33.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.445][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.446][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:33.447][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:33.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.448][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:33.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.452][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:33.453][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:33.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.454][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.455][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:33.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:33.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.458][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:33.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:33.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.460][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:33.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:33.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:33.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:33.487][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-10-02 21:41:33.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:33.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:33.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:33.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:33.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:33.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:33.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:33.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:33.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:33.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:33.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:33.517][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-10-02 21:41:33.517][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:33.518][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-10-02 21:41:33.519][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:33.520][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:33.521][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:33.521][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:33.522][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:33.523][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:33.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:33.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:33.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:33.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:33.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:33.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:33.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:33.532][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-10-02 21:41:33.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:33.535][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:33.536][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-10-02 21:41:33.936][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-10-02 21:41:34.336][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:34.339][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-10-02 21:41:34.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-10-02 21:41:34.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-10-02 21:41:34.344][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:34.345][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:34.346][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:34.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:34.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:34.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:34.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:34.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:34.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:34.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:34.356][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.358][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.362][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:34.363][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:34.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.365][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:34.365][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:34.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.368][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:34.368][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:34.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.370][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.371][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:34.371][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:34.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.373][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:34.374][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:34.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.375][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.376][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:34.377][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.378][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.379][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:34.380][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:34.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.381][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.382][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:34.383][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:34.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.384][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:34.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:34.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.388][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:34.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:34.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.390][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.391][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:34.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:34.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.394][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:34.394][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:34.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.396][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:34.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:34.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:34.423][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-10-02 21:41:34.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:34.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:34.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:34.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:34.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:34.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:34.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:34.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:34.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:34.453][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[2024-10-02 21:41:34.453][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-10-02 21:41:34.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:34.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-10-02 21:41:34.457][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:34.457][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:34.458][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:34.459][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:34.460][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:34.460][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:34.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:34.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:34.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:34.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:34.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:34.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:34.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:34.559][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-10-02 21:41:34.562][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:34.562][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:34.563][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-10-02 21:41:34.964][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-10-02 21:41:35.366][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-02 21:41:35.368][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-02 21:41:35.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-10-02 21:41:35.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-10-02 21:41:35.373][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-10-02 21:41:35.374][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:35.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:35.376][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:35.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:35.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:35.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:35.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:35.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:35.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:35.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:35.385][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.391][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:35.392][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:35.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.393][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.394][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:35.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:35.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.397][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:35.397][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:35.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.399][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:35.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.403][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:35.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:35.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.404][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:35.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.408][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:35.409][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:35.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.410][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:35.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.414][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:35.414][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:35.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.416][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:35.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:35.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.419][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:35.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:35.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.425][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:35.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:35.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.427][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.430][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:35.431][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:35.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.432][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:35.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:35.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.436][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:35.437][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:35.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.438][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.439][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:35.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.442][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:35.442][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:35.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.444][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:35.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:35.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:35.483][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-10-02 21:41:35.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:35.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:35.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:35.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:35.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:35.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:35.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:35.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:35.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:35.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:35.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:35.499][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-10-02 21:41:35.500][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:35.501][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-10-02 21:41:35.502][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:35.503][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:35.504][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:35.504][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:35.505][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:35.506][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:35.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:35.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:35.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:35.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:35.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:35.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:35.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:35.515][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-10-02 21:41:35.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:35.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:35.518][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-10-02 21:41:35.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-10-02 21:41:36.322][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:36.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-10-02 21:41:36.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-10-02 21:41:36.329][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-10-02 21:41:36.330][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:36.331][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:36.332][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:36.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:36.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:36.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:36.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:36.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:36.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:36.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:36.342][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.343][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.344][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.348][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:36.349][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:36.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.350][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.351][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:36.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:36.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.354][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:36.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:36.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.356][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:36.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:36.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.360][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:36.360][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:36.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.362][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:36.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.365][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:36.366][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:36.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:36.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.371][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:36.371][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:36.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.373][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.373][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:36.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:36.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.376][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:36.377][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.378][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.379][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:36.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.382][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:36.382][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:36.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.384][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:36.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:36.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.387][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:36.388][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:36.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.389][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:36.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.393][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:36.398][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:36.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.403][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:36.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:36.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:36.407][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:36.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.408][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:36.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:36.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:36.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:36.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:36.439][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-10-02 21:41:36.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:36.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:36.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:36.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:36.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:36.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:36.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:36.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:36.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:36.456][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-10-02 21:41:36.456][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:36.457][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-10-02 21:41:36.458][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:36.459][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:36.460][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:36.461][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:36.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:36.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:36.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:36.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:36.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:36.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:36.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:36.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:36.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:36.471][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-10-02 21:41:36.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:36.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:36.475][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-10-02 21:41:36.877][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-10-02 21:41:37.280][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:37.282][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-10-02 21:41:37.285][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-10-02 21:41:37.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-10-02 21:41:37.288][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:37.289][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:37.290][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:37.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:37.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:37.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:37.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:37.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:37.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:37.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:37.300][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.302][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.306][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:37.306][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:37.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:37.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.311][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:37.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:37.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.314][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:37.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:37.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.317][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:37.318][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:37.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.319][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:37.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.323][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:37.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:37.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.325][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:37.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:37.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.328][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:37.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:37.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.338][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.339][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:37.340][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.342][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:37.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.345][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:37.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:37.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.347][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:37.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:37.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.353][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:37.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:37.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.356][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:37.357][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:37.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.358][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:37.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:37.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:37.363][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:37.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.364][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.365][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:37.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:37.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:37.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:37.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:37.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:37.395][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-10-02 21:41:37.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:37.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:37.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:37.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:37.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:37.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:37.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:37.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:37.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:37.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:37.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:37.411][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-10-02 21:41:37.412][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:37.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-10-02 21:41:37.414][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:37.415][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:37.415][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:37.416][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:37.417][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:37.417][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:37.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:37.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:37.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:37.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:37.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:37.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:37.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:37.426][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-10-02 21:41:37.428][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:37.429][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:37.430][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-10-02 21:41:37.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-10-02 21:41:38.231][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:38.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-10-02 21:41:38.236][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-10-02 21:41:38.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-10-02 21:41:38.239][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:38.240][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:38.240][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:38.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:38.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:38.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:38.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:38.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:38.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:38.248][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.TRACE[2024-10-02 21:41:38.250][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.251][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.252][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.256][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:38.257][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:38.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.258][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.267][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:38.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:38.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.269][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:38.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:38.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.272][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:38.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:38.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.275][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:38.276][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:38.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.277][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:38.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:38.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.281][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:38.282][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:38.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.283][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:38.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:38.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.287][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:38.287][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:38.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.289][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.289][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:38.290][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.292][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.292][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:38.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.295][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:38.296][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:38.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.297][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:38.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:38.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.301][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:38.301][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:38.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.303][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:38.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:38.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.306][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:38.307][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:38.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.309][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:38.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:38.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.312][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:38.313][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:38.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.314][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:38.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:38.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:38.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:38.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:38.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:38.344][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-10-02 21:41:38.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:38.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:38.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:38.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:38.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:38.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:38.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:38.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:38.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:38.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:38.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:38.361][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-10-02 21:41:38.362][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:38.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-10-02 21:41:38.364][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:38.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:38.365][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:38.366][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:38.367][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:38.367][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:38.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:38.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:38.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:38.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:38.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:38.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:38.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:38.376][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-10-02 21:41:38.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:38.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:38.380][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-10-02 21:41:38.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-10-02 21:41:39.182][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:39.184][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-10-02 21:41:39.187][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-10-02 21:41:39.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-10-02 21:41:39.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:39.199][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:39.200][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:39.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:39.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:39.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:39.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:39.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:39.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:39.208][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.TRACE[2024-10-02 21:41:39.210][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.211][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.212][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.216][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:39.217][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:39.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.218][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.219][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:39.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:39.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.222][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:39.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:39.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.224][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.227][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:39.228][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:39.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.229][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:39.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:39.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.233][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:39.234][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:39.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.235][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:39.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:39.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.238][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:39.239][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:39.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.240][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.241][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:39.242][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.244][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:39.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.247][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:39.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:39.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.249][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:39.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:39.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.252][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:39.253][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:39.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:39.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:39.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.258][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:39.259][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:39.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.260][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.261][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:39.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:39.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:39.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:39.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:39.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:39.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:39.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:39.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:39.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:39.297][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-10-02 21:41:39.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:39.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:39.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:39.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:39.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:39.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:39.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:39.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:39.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:39.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:39.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:39.314][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-10-02 21:41:39.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:39.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-10-02 21:41:39.317][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:39.318][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:39.324][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:39.324][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:39.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:39.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:39.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:39.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:39.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:39.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:39.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:39.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:39.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:39.335][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-10-02 21:41:39.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:39.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:39.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-10-02 21:41:39.743][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-10-02 21:41:40.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:40.151][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-10-02 21:41:40.154][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-10-02 21:41:40.156][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-10-02 21:41:40.157][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:40.158][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:40.158][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:40.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:40.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:40.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:40.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:40.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:40.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:40.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:40.169][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.169][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.174][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:40.175][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:40.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.176][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.177][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:40.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:40.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.180][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:40.181][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:40.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:40.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:40.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.186][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:40.187][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:40.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.188][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:40.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:40.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:40.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:40.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.193][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:40.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.197][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:40.198][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:40.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.199][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.200][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:40.201][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.202][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.203][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:40.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.206][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:40.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:40.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.208][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:40.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:40.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.211][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:40.212][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:40.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:40.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.217][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:40.218][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:40.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.219][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.220][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:40.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:40.223][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:40.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:40.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:40.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:40.289][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-10-02 21:41:40.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:40.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:40.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:40.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:40.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:40.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:40.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:40.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:40.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:40.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:40.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:40.307][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-10-02 21:41:40.307][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:40.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-10-02 21:41:40.309][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:40.310][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:40.311][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:40.312][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:40.312][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:40.313][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:40.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:40.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:40.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:40.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:40.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:40.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:40.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:40.322][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-10-02 21:41:40.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:40.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:40.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-10-02 21:41:40.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-10-02 21:41:41.128][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:41.130][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-10-02 21:41:41.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-10-02 21:41:41.135][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-10-02 21:41:41.136][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:41.137][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:41.138][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:41.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:41.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:41.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:41.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:41.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:41.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:41.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:41.152][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.153][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.154][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.165][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:41.166][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.167][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:41.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:41.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.174][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:41.174][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:41.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.181][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:41.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:41.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.186][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:41.187][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:41.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.188][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:41.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.192][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:41.193][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:41.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.194][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:41.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.198][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:41.199][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:41.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.200][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.201][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:41.202][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.203][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.207][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:41.207][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:41.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.208][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:41.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.212][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:41.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:41.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.214][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:41.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:41.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.218][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:41.219][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:41.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.220][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.221][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:41.224][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:41.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:41.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:41.265][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-10-02 21:41:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:41.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:41.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:41.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:41.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:41.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:41.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:41.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:41.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:41.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:41.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:41.282][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-10-02 21:41:41.282][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:41.284][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-10-02 21:41:41.284][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:41.285][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:41.286][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:41.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:41.287][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:41.288][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:41.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:41.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:41.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:41.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:41.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:41.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:41.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:41.297][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-10-02 21:41:41.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:41.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:41.301][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-10-02 21:41:41.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-10-02 21:41:42.102][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:42.104][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-10-02 21:41:42.106][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-10-02 21:41:42.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-10-02 21:41:42.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:42.109][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:42.110][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:42.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:42.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:42.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:42.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:42.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:42.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:42.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:42.120][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.120][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.125][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:42.126][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:42.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.127][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.128][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:42.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:42.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:42.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:42.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.133][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:42.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:42.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.137][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:42.137][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:42.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.139][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:42.140][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:42.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.142][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.143][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:42.143][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:42.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.145][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.145][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:42.146][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.147][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.148][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.151][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:42.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:42.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.153][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:42.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:42.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.157][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:42.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:42.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.159][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:42.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:42.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.162][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:42.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:42.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.164][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:42.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.176][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:42.176][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:42.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.178][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:42.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:42.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:42.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:42.206][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-10-02 21:41:42.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:42.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:42.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:42.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:42.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:42.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:42.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:42.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:42.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:42.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:42.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:42.222][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-10-02 21:41:42.223][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:42.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-10-02 21:41:42.225][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:42.226][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:42.226][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:42.227][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:42.228][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:42.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:42.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:42.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:42.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:42.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:42.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:42.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:42.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:42.237][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-10-02 21:41:42.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:42.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:42.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-10-02 21:41:42.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-10-02 21:41:43.038][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:43.040][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-10-02 21:41:43.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-10-02 21:41:43.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-10-02 21:41:43.045][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:43.046][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:43.046][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:43.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:43.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:43.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:43.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:43.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:43.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:43.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:43.055][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.056][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.057][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.061][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:43.062][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:43.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.063][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:43.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:43.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.067][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:43.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:43.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:43.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:43.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:43.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:43.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.074][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:43.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:43.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.077][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.078][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:43.079][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:43.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.080][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.081][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:43.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:43.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:43.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:43.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.088][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:43.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.099][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:43.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:43.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.101][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:43.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:43.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.105][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:43.106][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:43.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.108][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:43.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.111][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:43.112][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:43.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:43.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:43.141][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-10-02 21:41:43.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:43.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:43.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:43.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:43.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:43.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:43.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:43.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:43.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:43.156][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-10-02 21:41:43.157][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:43.158][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-10-02 21:41:43.159][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:43.160][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:43.160][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:43.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:43.162][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:43.162][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:43.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:43.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:43.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:43.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:43.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:43.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:43.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:43.171][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-10-02 21:41:43.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:43.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:43.175][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-10-02 21:41:43.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-10-02 21:41:43.979][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:43.981][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-10-02 21:41:43.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-10-02 21:41:43.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-10-02 21:41:43.986][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:43.986][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:43.987][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:43.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:43.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:43.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:43.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:43.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:43.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:43.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:43.997][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:43.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:43.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:43.999][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:43.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.002][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:44.003][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:44.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.004][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.005][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:44.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:44.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.008][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:44.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:44.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.010][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:44.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.013][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:44.014][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:44.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.015][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:44.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.020][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.021][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.029][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.033][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:44.034][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:44.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.036][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:44.037][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.038][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.042][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.044][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.047][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:44.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:44.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.049][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:44.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:44.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.053][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:44.054][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:44.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.055][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.056][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:44.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:44.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.059][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:44.059][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:44.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.060][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:44.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:44.090][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-10-02 21:41:44.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:44.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:44.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:44.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:44.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:44.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:44.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:44.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:44.106][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-10-02 21:41:44.107][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:44.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-10-02 21:41:44.109][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:44.109][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:44.110][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:44.111][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:44.112][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:44.112][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:44.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:44.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:44.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:44.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:44.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:44.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:44.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:44.121][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-10-02 21:41:44.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:44.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:44.125][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-10-02 21:41:44.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-10-02 21:41:44.925][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:44.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-10-02 21:41:44.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-10-02 21:41:44.930][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-10-02 21:41:44.931][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:44.932][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:44.933][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:44.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:44.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:44.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:44.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:44.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:44.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:44.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:44.942][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.942][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.944][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:44.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:44.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.954][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:44.955][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:44.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.957][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:44.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.960][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:44.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:44.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.962][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:44.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:44.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.966][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:44.966][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:44.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.968][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:44.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.973][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:44.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:44.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.979][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.980][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:44.981][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.982][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.983][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:44.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:44.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.986][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.987][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:44.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:44.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:44.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.993][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:44.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:44.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:44.997][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:44.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:44.998][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:44.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:45.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:45.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.002][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:45.003][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:45.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.004][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:45.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:45.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:45.034][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-10-02 21:41:45.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:45.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:45.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:45.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:45.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:45.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:45.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:45.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:45.051][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-10-02 21:41:45.051][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:45.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-10-02 21:41:45.053][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:45.054][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:45.055][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:45.056][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:45.056][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:45.057][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:45.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:45.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:45.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:45.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:45.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:45.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:45.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:45.066][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-10-02 21:41:45.068][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:45.069][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:45.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-10-02 21:41:45.471][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-10-02 21:41:45.876][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:45.881][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-10-02 21:41:45.884][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-10-02 21:41:45.885][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-10-02 21:41:45.886][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:45.887][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:45.888][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:45.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:45.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:45.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:45.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:45.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:45.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:45.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:45.898][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.899][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.900][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.904][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:45.905][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:45.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.907][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:45.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.909][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:45.910][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:45.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.911][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.912][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:45.916][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:45.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.917][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:45.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:45.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.921][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:45.921][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:45.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.923][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:45.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:45.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.926][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:45.927][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:45.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.928][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.929][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:45.930][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.931][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.932][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:45.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.935][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:45.936][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:45.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.937][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:45.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:45.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:45.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:45.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.942][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:45.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:45.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.946][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:45.947][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:45.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.948][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.949][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:45.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:45.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.952][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:45.953][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:45.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.954][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:45.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:45.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:45.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:45.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:45.984][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-10-02 21:41:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:45.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:45.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:45.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:45.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:45.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:45.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:45.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:45.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:46.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:46.000][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-10-02 21:41:46.006][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:46.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-10-02 21:41:46.008][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:46.009][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:46.010][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:46.011][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:46.011][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:46.012][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:46.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:46.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:46.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:46.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:46.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:46.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:46.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:46.021][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-10-02 21:41:46.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:46.024][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:46.025][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-10-02 21:41:46.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-10-02 21:41:46.822][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:46.823][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-10-02 21:41:46.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-10-02 21:41:46.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-10-02 21:41:46.828][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:46.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:46.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:46.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:46.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:46.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:46.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:46.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:46.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:46.837][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[2024-10-02 21:41:46.839][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.841][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.844][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:46.845][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:46.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.846][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:46.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.850][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:46.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:46.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.852][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:46.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:46.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.855][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:46.856][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:46.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.857][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:46.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:46.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.861][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:46.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:46.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.863][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:46.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.866][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:46.867][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:46.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.868][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.869][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:46.870][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.871][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.872][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:46.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:46.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.877][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:46.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:46.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.880][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:46.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:46.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:46.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:46.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.886][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:46.886][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:46.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.888][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:46.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.891][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:46.892][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:46.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.893][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.894][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:46.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:46.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:46.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:46.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:46.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:46.930][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-10-02 21:41:46.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:46.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:46.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:46.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:46.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:46.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:46.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:46.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:46.946][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-10-02 21:41:46.947][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:46.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-10-02 21:41:46.949][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:46.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:46.950][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:46.951][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:46.952][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:46.952][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:46.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:46.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:46.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:46.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:46.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:46.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:46.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:46.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-10-02 21:41:46.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:46.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:46.965][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-10-02 21:41:47.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-10-02 21:41:47.768][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:47.770][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-10-02 21:41:47.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-10-02 21:41:47.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-10-02 21:41:47.775][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:47.776][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:47.777][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:47.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:47.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:47.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:47.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:47.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:47.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:47.785][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.TRACE[2024-10-02 21:41:47.787][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.787][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.789][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.792][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:47.793][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:47.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.794][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.795][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:47.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:47.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.798][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:47.799][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:47.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.800][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:47.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:47.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:47.804][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:47.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.806][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:47.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:47.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.809][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:47.810][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:47.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.811][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:47.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:47.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.815][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:47.815][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:47.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.817][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.818][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:47.818][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.820][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.820][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:47.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:47.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.825][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:47.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:47.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.829][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:47.829][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:47.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.831][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:47.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:47.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.834][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:47.835][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:47.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.836][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.837][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:47.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:47.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.840][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:47.841][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:47.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.842][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:47.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:47.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:47.881][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-10-02 21:41:47.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:47.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:47.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:47.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:47.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:47.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:47.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:47.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:47.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:47.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:47.897][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-10-02 21:41:47.898][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:47.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-10-02 21:41:47.900][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:47.901][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:47.901][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:47.902][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:47.903][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:47.903][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:47.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:47.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:47.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:47.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:47.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:47.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:47.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:47.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-10-02 21:41:47.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:47.915][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:47.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-10-02 21:41:48.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-10-02 21:41:48.713][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:48.715][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-10-02 21:41:48.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-10-02 21:41:48.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-10-02 21:41:48.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:48.721][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:48.721][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:48.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:48.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:48.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:48.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:48.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:48.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:48.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:48.731][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.733][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.737][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:48.737][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:48.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.739][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.739][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:48.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:48.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.742][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:48.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:48.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.744][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:48.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:48.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.748][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:48.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:48.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.750][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:48.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:48.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:48.754][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:48.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.756][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:48.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.759][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:48.760][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:48.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.761][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.762][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:48.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.764][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.765][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:48.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:48.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:48.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.769][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:48.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:48.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:48.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:48.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.782][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:48.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:48.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.786][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:48.787][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:48.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.788][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:48.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:48.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.792][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:48.792][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:48.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.794][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.795][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:48.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:48.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:48.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:48.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:48.824][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-10-02 21:41:48.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:48.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:48.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:48.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:48.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:48.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:48.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:48.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:48.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:48.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:48.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:48.840][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-10-02 21:41:48.841][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:48.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-10-02 21:41:48.843][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:48.843][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:48.844][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:48.845][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:48.846][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:48.846][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:48.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:48.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:48.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:48.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:48.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:48.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:48.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:48.855][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-10-02 21:41:48.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:48.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:48.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-10-02 21:41:49.256][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-10-02 21:41:49.652][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:49.654][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-10-02 21:41:49.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-10-02 21:41:49.658][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-10-02 21:41:49.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:49.660][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:49.660][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:49.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:49.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:49.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:49.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:49.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:49.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:49.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:49.669][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.670][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.671][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.675][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:49.676][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:49.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.677][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:49.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.681][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:49.681][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:49.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.682][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.683][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:49.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:49.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:49.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.688][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:49.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:49.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.699][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:49.700][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:49.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.701][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.704][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:49.705][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:49.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.707][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.707][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:49.708][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.709][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:49.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.713][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:49.714][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:49.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.715][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:49.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.719][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:49.720][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:49.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.721][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.724][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:49.725][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:49.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.726][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:49.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.730][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:49.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:49.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.732][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:49.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:49.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:49.762][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-10-02 21:41:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:49.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:49.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:49.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:49.788][private$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[2024-10-02 21:41:50.330][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[2024-10-02 21:41:51.032][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:51.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-02 21:41:51.037][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-02 21:41:51.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.089][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.TRACE[2024-10-02 21:41:51.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.194][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.TRACE[2024-10-02 21:41:51.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.239][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.TRACE[2024-10-02 21:41:51.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:51.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:51.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:51.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:51.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:51.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:51.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:51.363][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[2024-10-02 21:41:51.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:51.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:51.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:51.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:51.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:51.412][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[2024-10-02 21:41:51.415][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:51.415][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:51.417][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:41:51.814][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:41:52.213][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:52.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-10-02 21:41:52.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-10-02 21:41:52.227][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:52.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:52.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:52.231][private$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[2024-10-02 21:41:52.630][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[2024-10-02 21:41:53.031][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:53.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-10-02 21:41:53.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-10-02 21:41:53.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:53.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:53.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:53.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:53.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:53.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:53.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:53.044][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-10-02 21:41:53.045][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:53.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-10-02 21:41:53.047][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:53.048][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:53.048][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:53.049][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:53.050][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:53.050][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:53.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:53.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:53.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:53.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:53.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:53.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:53.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:53.059][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-10-02 21:41:53.061][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:53.062][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:53.063][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-10-02 21:41:53.461][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-10-02 21:41:53.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:53.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-10-02 21:41:53.864][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-10-02 21:41:53.866][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-10-02 21:41:53.867][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:53.867][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:53.868][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:53.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:53.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:53.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:53.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:53.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:53.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:53.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:53.877][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.879][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.883][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:53.884][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:53.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.885][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.886][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:53.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.889][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:53.889][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:53.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.891][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:53.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:53.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.894][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:53.895][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:53.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.896][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:53.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:53.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.900][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:53.901][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:53.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.902][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.905][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:53.906][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:53.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.907][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.911][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:53.912][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:53.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.913][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.914][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:53.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:53.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.917][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.919][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.922][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:53.923][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:53.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.924][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:53.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.928][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:53.928][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:53.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.930][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:53.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:53.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.933][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:53.934][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:53.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.935][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.941][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:53.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:53.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:53.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:53.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:53.976][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-10-02 21:41:53.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:53.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:53.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:53.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:53.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:53.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:53.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:53.991][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[2024-10-02 21:41:53.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:53.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:53.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:53.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:54.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:54.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:54.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:54.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:54.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:54.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:54.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:54.007][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-10-02 21:41:54.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:41:54.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-10-02 21:41:54.010][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:41:54.010][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:41:54.011][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:41:54.012][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:41:54.013][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:41:54.013][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:41:54.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:54.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:54.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:54.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:54.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:54.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:54.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:54.022][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-10-02 21:41:54.024][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:54.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:54.026][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-10-02 21:41:54.429][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-10-02 21:41:54.827][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:54.829][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-10-02 21:41:54.837][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-10-02 21:41:54.841][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-10-02 21:41:54.843][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:41:54.844][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:41:54.848][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:41:54.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:54.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:54.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:54.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:54.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:54.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:54.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:54.870][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.871][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.875][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.883][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:54.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:54.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.886][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.887][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:41:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:41:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.894][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:54.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:54.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.900][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:41:54.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:41:54.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.908][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:54.908][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:54.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.910][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:41:54.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:41:54.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.924][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:54.925][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:54.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.927][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:41:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:41:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:54.931][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:41:54.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.933][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.934][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:54.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:54.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.936][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:41:54.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:54.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.940][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.941][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.942][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.946][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:54.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:54.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.948][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:41:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:41:54.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.952][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:54.953][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:54.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.954][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:41:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:41:54.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.958][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:54.958][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:54.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.960][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:41:54.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:41:54.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:54.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:41:54.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:41:54.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:54.992][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-10-02 21:41:54.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:54.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:54.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:54.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.016][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[2024-10-02 21:41:55.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:55.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:55.020][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:55.021][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 21:41:55.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.198][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.TRACE[2024-10-02 21:41:55.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.213][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.TRACE[2024-10-02 21:41:55.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.232][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[2024-10-02 21:41:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.247][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[2024-10-02 21:41:55.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.439][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[2024-10-02 21:41:55.441][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:55.442][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-02 21:41:55.443][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:55.444][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-02 21:41:55.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.452][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[2024-10-02 21:41:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.467][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[2024-10-02 21:41:55.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.517][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[2024-10-02 21:41:55.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.710][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.TRACE[2024-10-02 21:41:55.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.725][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.TRACE[2024-10-02 21:41:55.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:55.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.794][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 21:41:55.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 21:41:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:55.802][biodb::testThat]
biodb.INFO [2024-10-02 21:41:55.803][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-02 21:41:55.803][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:55.804][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:55.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 21:41:55.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 21:41:55.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:55.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:55.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:55.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:55.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:55.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:55.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:55.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:55.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:55.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:55.830][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[2024-10-02 21:41:55.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:55.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:55.835][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:41:56.238][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:41:56.642][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:56.645][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-02 21:41:56.649][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-02 21:41:56.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:56.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:56.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:56.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:56.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:56.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:56.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:56.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:56.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:56.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:56.667][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:56.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:56.670][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:56.672][private$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[2024-10-02 21:41:57.081][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[2024-10-02 21:41:57.484][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:57.486][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-02 21:41:57.489][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-02 21:41:57.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:57.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:57.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:57.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:57.523][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:41:57.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.537][private$selectFields]
biodb.TRACE[2024-10-02 21:41:57.538][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:57.539][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:57.539][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.540][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.541][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.542][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.543][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.545][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.545][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.546][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.547][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.549][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.549][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.565][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 21:41:57.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:57.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.579][private$selectFields]
biodb.TRACE[2024-10-02 21:41:57.580][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:57.580][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:57.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.584][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.584][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.585][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.586][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.588][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.588][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.589][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.590][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.591][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:57.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.600][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:41:57.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:57.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.627][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.627][private$selectFields]
biodb.TRACE[2024-10-02 21:41:57.628][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:57.629][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:57.629][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.630][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.631][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.632][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.634][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.635][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.636][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:57.637][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.639][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.640][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:57.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:57.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.649][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 21:41:57.649][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:41:57.650][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:41:57.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:57.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:57.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:57.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:57.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:57.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:57.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:57.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:57.715][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[2024-10-02 21:41:57.718][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:57.718][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:57.720][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:41:58.151][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:41:58.550][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:58.552][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-10-02 21:41:58.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-10-02 21:41:58.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:41:58.570][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:41:58.571][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:41:58.572][private$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[2024-10-02 21:41:58.972][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[2024-10-02 21:41:59.374][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:41:59.377][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-10-02 21:41:59.380][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-10-02 21:41:59.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.383][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.421][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[2024-10-02 21:41:59.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.447][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:41:59.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.477][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.478][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.486][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.490][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.491][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.494][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.494][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.495][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.498][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.508][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 21:41:59.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.545][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.546][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.546][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.547][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.549][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.550][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.551][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.552][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.553][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.554][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.561][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.564][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.565][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.574][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:41:59.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.588][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.588][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.589][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.590][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.593][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.594][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.594][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.596][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.596][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.597][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.603][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.604][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.606][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.616][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 21:41:59.617][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:41:59.617][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:41:59.623][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 21:41:59.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 21:41:59.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:41:59.628][biodb::testThat]
biodb.INFO [2024-10-02 21:41:59.629][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-02 21:41:59.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:41:59.630][biodb::testThat]
biodb.TRACE[2024-10-02 21:41:59.633][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 21:41:59.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 21:41:59.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:59.656][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[2024-10-02 21:41:59.659][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:59.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-02 21:41:59.660][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:59.661][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-02 21:41:59.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.679][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[2024-10-02 21:41:59.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:59.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-02 21:41:59.683][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:59.684][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-02 21:41:59.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.707][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.TRACE[2024-10-02 21:41:59.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:41:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.716][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:41:59.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.724][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.TRACE[2024-10-02 21:41:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.736][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.737][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.737][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.738][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.739][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.740][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.742][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.742][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.744][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.746][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.747][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.749][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.749][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.758][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 21:41:59.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.773][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.773][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.774][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.775][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.777][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.779][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.780][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.781][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.781][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.784][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.785][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.794][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:41:59.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.807][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.808][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.809][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.810][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.811][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.813][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.814][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.815][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.816][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.817][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.818][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.820][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.829][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 21:41:59.830][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:41:59.830][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:41:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:41:59.863][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[2024-10-02 21:41:59.865][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:59.866][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-02 21:41:59.867][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:59.868][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-02 21:41:59.870][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[2024-10-02 21:41:59.873][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:41:59.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-02 21:41:59.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:41:59.875][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-02 21:41:59.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:41:59.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:41:59.922][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:41:59.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.930][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.TRACE[2024-10-02 21:41:59.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.936][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.936][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.937][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.938][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.940][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.941][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.942][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.944][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.944][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.945][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.946][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.948][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.948][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.957][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 21:41:59.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:41:59.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:41:59.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:41:59.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:41:59.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:41:59.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:41:59.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.970][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.971][private$selectFields]
biodb.TRACE[2024-10-02 21:41:59.971][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:41:59.972][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:41:59.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.981][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.984][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.985][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.985][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:41:59.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.987][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.988][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.989][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:41:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:41:59.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:41:59.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:41:59.998][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:41:59.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:41:59.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.012][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.012][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.013][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.016][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.019][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.020][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.020][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.023][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.023][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 21:42:00.033][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:42:00.034][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:42:00.039][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 21:42:00.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 21:42:00.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:42:00.044][biodb::testThat]
biodb.INFO [2024-10-02 21:42:00.045][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-02 21:42:00.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:00.046][biodb::testThat]
biodb.TRACE[2024-10-02 21:42:00.048][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-02 21:42:00.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-02 21:42:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.070][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[2024-10-02 21:42:00.072][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[2024-10-02 21:42:00.074][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:00.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-02 21:42:00.076][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:00.077][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-02 21:42:00.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.085][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.TRACE[2024-10-02 21:42:00.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.094][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[2024-10-02 21:42:00.101][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:00.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-02 21:42:00.103][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:00.104][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-02 21:42:00.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:00.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.136][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:42:00.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.150][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.150][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.154][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.155][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.157][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.158][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.160][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.161][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.161][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-02 21:42:00.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.183][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.184][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.184][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.185][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.186][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.188][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.191][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.192][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.193][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.194][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.195][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.195][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.204][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:42:00.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.211][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.TRACE[2024-10-02 21:42:00.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.222][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.223][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.224][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.226][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.228][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.230][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.235][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.244][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-02 21:42:00.245][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:42:00.245][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:42:00.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:00.279][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[2024-10-02 21:42:00.281][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:00.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-02 21:42:00.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:00.284][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-02 21:42:00.286][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[2024-10-02 21:42:00.288][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:00.289][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-02 21:42:00.290][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:00.291][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-02 21:42:00.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:00.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:00.343][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-02 21:42:00.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.357][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.357][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.358][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.359][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.359][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.360][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.361][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.362][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.363][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.365][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.365][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.366][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.367][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.369][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.369][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.378][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-02 21:42:00.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:00.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.391][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.392][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.393][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.393][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.396][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.397][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.399][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.400][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.400][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.404][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.413][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-02 21:42:00.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.419][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[2024-10-02 21:42:00.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.426][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.426][private$selectFields]
biodb.TRACE[2024-10-02 21:42:00.427][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-02 21:42:00.428][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-02 21:42:00.428][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.431][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.432][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.434][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.434][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.435][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-02 21:42:00.436][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.436][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.438][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.438][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-02 21:42:00.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:00.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:00.447][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-02 21:42:00.448][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-02 21:42:00.448][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-02 21:42:00.466][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-02 21:42:00.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-02 21:42:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-02 21:42:00.471][biodb::testThat]
biodb.INFO [2024-10-02 21:42:00.472][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-10-02 21:42:00.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:00.473][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:00.475][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-02 21:42:00.475][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:42:00.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-02 21:42:00.477][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:42:00.478][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:42:00.479][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:42:00.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:00.480][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:42:00.481][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:42:00.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:00.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:00.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:00.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:00.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:00.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:00.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:00.490][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-10-02 21:42:00.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:00.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:00.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-10-02 21:42:00.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-10-02 21:42:01.297][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:01.299][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-10-02 21:42:01.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-10-02 21:42:01.304][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-10-02 21:42:01.305][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:42:01.306][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:42:01.307][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:42:01.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:01.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:01.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:01.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:01.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:01.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:01.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:01.317][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.317][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.319][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.322][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:01.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:01.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.324][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.325][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:01.326][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:01.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.327][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.328][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:01.329][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:01.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.330][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.331][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:01.332][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:01.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.333][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.334][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:01.335][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:01.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.336][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.337][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:01.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:01.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.340][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:01.341][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:01.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.342][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.343][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:01.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:01.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.345][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.346][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:01.346][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:01.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.348][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.348][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:01.349][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:01.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.351][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:01.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:01.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:01.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:01.378][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-10-02 21:42:01.379][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-02 21:42:01.394][biodb::testThat]
biodb.INFO [2024-10-02 21:42:01.395][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-02 21:42:01.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:01.397][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:01.404][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-10-02 21:42:01.405][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-10-02 21:42:01.406][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-10-02 21:42:01.407][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-10-02 21:42:01.408][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-10-02 21:42:01.409][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:42:01.410][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:42:01.410][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:01.411][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:42:01.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:42:01.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:01.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:01.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:01.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:01.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:01.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:01.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:01.422][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-10-02 21:42:01.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:01.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:01.425][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-10-02 21:42:02.129][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-10-02 21:42:02.527][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:02.529][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-10-02 21:42:02.532][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-10-02 21:42:02.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:02.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:02.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:02.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:02.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:02.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:02.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:02.541][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-10-02 21:42:02.543][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:02.544][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:02.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-10-02 21:42:02.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-10-02 21:42:03.344][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:03.351][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-10-02 21:42:03.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-10-02 21:42:03.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:03.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:03.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:03.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:03.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:03.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:03.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:03.367][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-10-02 21:42:03.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:03.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:03.371][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-10-02 21:42:03.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-10-02 21:42:04.165][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:04.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-10-02 21:42:04.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-10-02 21:42:04.172][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-10-02 21:42:04.173][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:42:04.174][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-10-02 21:42:04.175][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-10-02 21:42:04.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:04.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:04.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:04.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:04.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:04.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:04.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:04.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.187][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.190][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:04.191][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:04.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.192][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.193][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:04.194][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:04.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.195][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:04.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:04.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.198][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.201][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.202][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.203][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.204][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:04.205][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:04.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.206][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.207][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.208][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.209][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.210][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:04.211][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:04.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.212][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.213][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:04.213][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:04.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.215][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.216][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:04.216][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:04.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:04.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:04.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:04.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:04.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:04.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:04.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:04.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:04.263][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.269][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:04.269][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:04.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.271][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:04.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:04.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.274][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:04.275][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:04.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.276][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:04.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:04.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:04.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.282][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:04.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.286][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.286][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.288][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.291][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.292][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.293][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.294][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.297][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:04.298][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:04.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.299][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.300][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:04.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:04.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.303][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.305][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:04.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:04.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:04.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:04.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.314][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:04.315][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:04.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.316][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.317][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:04.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:04.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.320][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:04.321][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:04.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.322][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.323][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:04.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:04.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:04.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:04.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:04.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:04.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:04.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:04.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:04.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:04.360][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.361][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.362][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.366][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:04.367][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:04.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.368][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.369][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:04.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:04.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.372][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:04.373][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:04.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.374][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:04.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.378][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:04.379][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:04.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.380][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:04.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:04.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.384][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.384][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.386][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:04.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.390][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.392][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:04.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.395][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:04.396][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:04.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.398][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:04.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:04.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.401][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.401][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.403][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:04.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.406][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:04.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:04.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.408][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.412][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:04.413][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:04.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.415][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:04.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:04.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.418][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:04.418][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:04.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.420][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:04.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:04.473][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-10-02 21:42:04.474][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-02 21:42:04.475][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-02 21:42:04.492][biodb::testThat]
biodb.INFO [2024-10-02 21:42:04.493][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-10-02 21:42:04.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:04.494][biodb::testThat]
biodb.INFO [2024-10-02 21:42:04.512][biodb::testThat]
biodb.INFO [2024-10-02 21:42:04.512][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-10-02 21:42:04.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:04.514][biodb::testThat]
biodb.INFO [2024-10-02 21:42:04.519][biodb::testThat]
biodb.INFO [2024-10-02 21:42:04.520][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-10-02 21:42:04.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:04.521][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:04.523][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[2024-10-02 21:42:04.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:04.527][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:04.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:42:04.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:42:05.544][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:05.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-10-02 21:42:05.552][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-10-02 21:42:05.568][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:05.568][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:05.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:05.570][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:05.570][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:05.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:05.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:05.573][ef$get] fields variable is a list.
biodb.INFO [2024-10-02 21:42:05.574][biodb::testThat]
biodb.INFO [2024-10-02 21:42:05.574][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-02 21:42:05.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:05.576][biodb::testThat]
biodb.ERROR[2024-10-02 21:42:05.585][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-02 21:42:05.597][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-02 21:42:05.606][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 21:42:05.607][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 21:42:05.607][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 21:42:05.608][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 21:42:05.609][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:05.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:05.610][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.611][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 21:42:05.619][biodb::testContext]
biodb.INFO [2024-10-02 21:42:05.619][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:05.620][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-10-02 21:42:05.621][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:05.621][biodb::testContext]
biodb.INFO [2024-10-02 21:42:05.623][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:05.624][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:05.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:05.627][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 21:42:05.628][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.630][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[2024-10-02 21:42:05.631][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 21:42:05.631][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.643][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 21:42:05.644][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.647][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 21:42:05.648][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 21:42:05.649][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 21:42:05.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.651][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 21:42:05.652][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 21:42:05.652][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.655][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 21:42:05.656][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 21:42:05.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.658][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 21:42:05.659][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 21:42:05.660][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 21:42:05.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.662][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 21:42:05.663][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.665][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 21:42:05.666][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 21:42:05.667][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 21:42:05.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.669][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:05.670][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 21:42:05.671][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 21:42:05.671][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 21:42:05.672][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 21:42:05.673][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 21:42:05.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.675][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 21:42:05.676][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 21:42:05.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.678][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 21:42:05.679][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 21:42:05.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.682][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 21:42:05.682][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 21:42:05.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.685][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 21:42:05.685][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 21:42:05.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.688][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 21:42:05.689][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 21:42:05.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.691][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:05.692][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 21:42:05.695][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-10-02 21:42:05.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.698][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 21:42:05.698][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 21:42:05.699][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 21:42:05.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.702][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 21:42:05.703][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.704][self$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[2024-10-02 21:42:05.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:05.706][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.707][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.708][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.708][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:05.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:05.710][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.711][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 21:42:05.711][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:05.712][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:05.713][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:05.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:05.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:05.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.718][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:05.720][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:05.720][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.721][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.722][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 21:42:05.723][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.724][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:05.724][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.725][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:05.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.728][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:05.729][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:05.730][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.731][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 21:42:05.731][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:05.732][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:05.733][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:05.734][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:05.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:05.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.738][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.739][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:05.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:05.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.741][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.742][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 21:42:05.743][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.744][self$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[2024-10-02 21:42:05.744][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.745][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:05.746][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.746][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.747][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.748][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:05.749][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:05.750][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.750][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 21:42:05.751][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:05.752][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.752][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.753][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.754][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:05.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.755][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:05.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.764][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:05.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:05.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.767][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.768][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 21:42:05.769][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.770][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:05.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:05.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.774][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:05.775][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:05.776][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.777][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 21:42:05.777][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:05.778][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.779][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:05.779][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:05.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:05.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:05.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:05.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:05.784][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.785][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:05.786][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:05.786][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:05.787][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:05.788][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:05.789][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.789][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[2024-10-02 21:42:05.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.795][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.DEBUG[2024-10-02 21:42:05.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.822][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[2024-10-02 21:42:05.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:05.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:05.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:05.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:05.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:05.840][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[2024-10-02 21:42:05.840][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 21:42:05.841][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 21:42:05.842][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 21:42:05.843][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 21:42:05.844][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:05.845][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 21:42:05.846][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:05.847][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:05.848][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 21:42:05.849][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 21:42:05.850][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:05.851][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 21:42:05.852][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:05.853][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:05.854][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 21:42:05.855][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 21:42:05.856][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 21:42:05.857][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 21:42:05.857][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:05.858][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 21:42:05.859][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 21:42:05.860][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 21:42:05.861][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 21:42:05.862][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 21:42:05.863][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 21:42:05.864][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 21:42:05.865][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 21:42:05.866][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 21:42:05.867][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 21:42:05.868][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 21:42:05.869][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 21:42:06.044][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 21:42:06.045][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 21:42:06.046][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 21:42:06.047][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 21:42:06.048][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 21:42:06.049][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 21:42:06.050][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 21:42:06.051][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 21:42:06.052][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 21:42:06.053][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 21:42:06.054][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 21:42:06.055][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 21:42:06.056][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 21:42:06.057][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 21:42:06.057][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 21:42:06.058][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 21:42:06.059][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 21:42:06.060][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 21:42:06.061][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 21:42:06.062][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 21:42:06.063][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 21:42:06.064][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 21:42:06.065][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 21:42:06.066][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 21:42:06.067][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 21:42:06.067][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 21:42:06.068][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 21:42:06.069][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 21:42:06.070][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 21:42:06.071][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 21:42:06.072][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 21:42:06.073][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 21:42:06.074][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 21:42:06.075][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 21:42:06.076][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 21:42:06.077][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:06.077][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:06.078][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 21:42:06.079][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 21:42:06.080][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 21:42:06.081][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 21:42:06.082][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 21:42:06.083][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 21:42:06.084][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 21:42:06.085][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 21:42:06.086][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 21:42:06.087][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 21:42:06.088][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 21:42:06.089][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 21:42:06.089][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 21:42:06.090][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 21:42:06.091][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 21:42:06.092][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 21:42:06.093][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:06.094][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:06.095][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.096][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.154][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[2024-10-02 21:42:06.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:06.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:06.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:06.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:06.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:06.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:06.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:06.171][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:06.172][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 21:42:06.174][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:06.174][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 21:42:06.175][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:06.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:06.176][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:06.177][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:06.178][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:06.178][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 21:42:06.179][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 21:42:06.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:06.180][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:06.181][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 21:42:06.182][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 21:42:06.183][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:06.184][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:06.184][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:06.184][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:06.184][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 21:42:06.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:06.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:06.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:06.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:06.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:06.188][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:06.189][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:06.189][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 21:42:06.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:06.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:06.190][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:06.191][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 21:42:06.191][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 21:42:06.192][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:06.193][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:06.194][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 21:42:06.195][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:06.196][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:06.197][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:06.199][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 21:42:06.200][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 21:42:06.201][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 21:42:06.202][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 21:42:06.203][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:06.203][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:06.204][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 21:42:06.205][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 21:42:06.206][biodb::testThat]
biodb.INFO [2024-10-02 21:42:06.206][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-10-02 21:42:06.207][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:06.208][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:06.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 21:42:06.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:06.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:06.215][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-10-02 21:42:06.608][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-10-02 21:42:07.104][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:07.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-10-02 21:42:07.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-10-02 21:42:07.110][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[2024-10-02 21:42:07.112][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:07.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:07.114][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:42:07.516][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:42:07.915][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:07.917][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-10-02 21:42:07.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-10-02 21:42:07.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:07.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:07.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:07.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:07.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:07.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:07.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:07.929][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:42:07.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:07.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:07.933][private$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[2024-10-02 21:42:08.336][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[2024-10-02 21:42:08.740][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:08.742][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-10-02 21:42:08.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-10-02 21:42:08.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:08.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:08.790][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[2024-10-02 21:42:08.792][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:08.793][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-02 21:42:08.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:08.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-02 21:42:08.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:08.803][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[2024-10-02 21:42:08.805][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:08.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-02 21:42:08.807][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:08.808][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-02 21:42:08.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:08.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.822][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[2024-10-02 21:42:08.824][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[2024-10-02 21:42:08.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:08.827][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-02 21:42:08.828][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:08.829][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-02 21:42:08.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.836][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[2024-10-02 21:42:08.837][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[2024-10-02 21:42:08.839][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:08.840][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-02 21:42:08.841][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:08.842][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-02 21:42:08.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:08.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:08.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:08.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:08.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:08.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:08.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:08.851][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[2024-10-02 21:42:08.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:08.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:08.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:42:09.257][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:42:09.659][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:09.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-10-02 21:42:09.664][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-10-02 21:42:09.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:09.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:09.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:09.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:09.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:09.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:09.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 21:42:09.677][biodb::testThat]
biodb.INFO [2024-10-02 21:42:09.678][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-10-02 21:42:09.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:09.679][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:09.682][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:42:09.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:09.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:09.686][private$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[2024-10-02 21:42:10.088][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[2024-10-02 21:42:10.489][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:10.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-10-02 21:42:10.494][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-10-02 21:42:10.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:10.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:10.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:10.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:10.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:10.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:10.502][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[2024-10-02 21:42:10.505][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[2024-10-02 21:42:10.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:10.508][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:10.509][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-02 21:42:10.917][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-02 21:42:11.320][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:11.321][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-10-02 21:42:11.324][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-10-02 21:42:11.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:11.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 21:42:11.336][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 21:42:11.336][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 21:42:11.337][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 21:42:11.338][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 21:42:11.338][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.339][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.341][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-02 21:42:11.344][biodb::testContext]
biodb.INFO [2024-10-02 21:42:11.344][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:11.345][biodb::testContext] Test context - Test web services
biodb.INFO [2024-10-02 21:42:11.346][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:11.346][biodb::testContext]
biodb.INFO [2024-10-02 21:42:11.348][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:11.349][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:11.352][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:11.352][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 21:42:11.353][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.355][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 21:42:11.356][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.358][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 21:42:11.359][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.362][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 21:42:11.362][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 21:42:11.363][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 21:42:11.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.365][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 21:42:11.366][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 21:42:11.367][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.369][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 21:42:11.370][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 21:42:11.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.372][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 21:42:11.372][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 21:42:11.373][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 21:42:11.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.375][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 21:42:11.376][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.379][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 21:42:11.379][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 21:42:11.380][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 21:42:11.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.382][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:11.383][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 21:42:11.384][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 21:42:11.384][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 21:42:11.385][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 21:42:11.386][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 21:42:11.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.388][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 21:42:11.389][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 21:42:11.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.391][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 21:42:11.392][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 21:42:11.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.394][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 21:42:11.395][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 21:42:11.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.397][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.DEBUG[2024-10-02 21:42:11.397][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 21:42:11.398][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 21:42:11.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.400][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 21:42:11.401][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 21:42:11.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.403][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:11.404][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 21:42:11.407][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-10-02 21:42:11.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.410][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 21:42:11.411][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 21:42:11.411][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 21:42:11.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.414][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 21:42:11.415][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.416][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 21:42:11.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:11.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.419][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.419][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.421][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:11.421][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:11.422][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.423][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 21:42:11.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:11.424][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:11.425][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:11.426][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:11.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.428][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:11.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.430][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.430][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:11.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:11.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.433][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.434][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 21:42:11.435][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.436][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:11.436][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.444][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:11.445][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.447][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:11.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:11.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.449][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 21:42:11.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:11.451][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.451][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.452][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:11.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:11.452][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:11.452][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:11.452][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:11.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:11.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.455][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:11.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.456][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.457][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.458][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:11.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:11.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.460][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.460][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 21:42:11.461][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.462][self$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[2024-10-02 21:42:11.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:11.464][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.465][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.465][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.467][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:11.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:11.468][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.469][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 21:42:11.469][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:11.470][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.471][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.471][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.472][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:11.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:11.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.476][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:11.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:11.478][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.479][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.479][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 21:42:11.480][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.481][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:11.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:11.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.486][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:11.486][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:11.487][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.487][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 21:42:11.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:11.489][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.490][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:11.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.492][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:11.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.494][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.495][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.496][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:11.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:11.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.497][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:11.498][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:11.499][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.502][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[2024-10-02 21:42:11.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.528][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[2024-10-02 21:42:11.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.549][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 21:42:11.550][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 21:42:11.555][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 21:42:11.556][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 21:42:11.556][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:11.557][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 21:42:11.558][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:11.559][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:11.560][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 21:42:11.561][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 21:42:11.562][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:11.563][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 21:42:11.564][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:11.565][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:11.566][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 21:42:11.567][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 21:42:11.567][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 21:42:11.568][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 21:42:11.569][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:11.570][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 21:42:11.571][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 21:42:11.572][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 21:42:11.573][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 21:42:11.574][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 21:42:11.575][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 21:42:11.576][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 21:42:11.577][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 21:42:11.578][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 21:42:11.578][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 21:42:11.579][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 21:42:11.580][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 21:42:11.581][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 21:42:11.582][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 21:42:11.583][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 21:42:11.584][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 21:42:11.585][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 21:42:11.586][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 21:42:11.587][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 21:42:11.588][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 21:42:11.588][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 21:42:11.589][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 21:42:11.590][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 21:42:11.591][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 21:42:11.592][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 21:42:11.593][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 21:42:11.594][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 21:42:11.595][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 21:42:11.596][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 21:42:11.597][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 21:42:11.598][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 21:42:11.599][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 21:42:11.599][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 21:42:11.600][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 21:42:11.601][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 21:42:11.602][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 21:42:11.603][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 21:42:11.604][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 21:42:11.605][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 21:42:11.606][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 21:42:11.607][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 21:42:11.608][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 21:42:11.609][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 21:42:11.609][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 21:42:11.610][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 21:42:11.611][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 21:42:11.612][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 21:42:11.613][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:11.614][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:11.615][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 21:42:11.616][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 21:42:11.617][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 21:42:11.618][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 21:42:11.619][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 21:42:11.619][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 21:42:11.620][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 21:42:11.621][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 21:42:11.622][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 21:42:11.623][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 21:42:11.624][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 21:42:11.625][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 21:42:11.626][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 21:42:11.627][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 21:42:11.628][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 21:42:11.629][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 21:42:11.630][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:11.631][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:11.631][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.632][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.633][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.DEBUG[2024-10-02 21:42:11.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.682][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[2024-10-02 21:42:11.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.697][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[2024-10-02 21:42:11.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:11.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:11.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:11.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:11.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:11.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:11.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:11.706][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:11.707][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 21:42:11.709][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.709][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.710][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:11.711][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.712][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.713][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.713][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 21:42:11.714][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 21:42:11.715][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:11.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.716][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 21:42:11.716][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 21:42:11.717][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 21:42:11.718][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:11.718][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:11.718][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:11.718][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:11.719][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 21:42:11.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.721][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:11.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:11.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:11.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:11.723][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:11.723][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 21:42:11.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:11.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:11.725][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:11.726][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 21:42:11.726][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 21:42:11.727][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:11.728][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:11.729][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 21:42:11.730][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:11.731][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:11.732][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:11.734][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 21:42:11.735][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 21:42:11.736][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 21:42:11.737][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 21:42:11.738][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:11.738][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:11.739][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 21:42:11.740][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 21:42:11.741][biodb::testThat]
biodb.INFO [2024-10-02 21:42:11.741][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-10-02 21:42:11.742][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:11.743][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:11.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 21:42:11.748][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:11.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 21:42:11.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:11.751][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 21:42:11.753][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-02 21:42:11.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:11.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:11.757][private$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[2024-10-02 21:42:12.164][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[2024-10-02 21:42:12.563][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:12.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-10-02 21:42:12.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-10-02 21:42:12.585][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 21:42:12.586][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 21:42:12.587][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 21:42:12.587][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 21:42:12.591][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.592][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.593][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.596][FUN] Functions in observer BiodbConfig: [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 [2024-10-02 21:42:12.599][biodb::testContext]
biodb.INFO [2024-10-02 21:42:12.605][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:12.610][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-10-02 21:42:12.611][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-02 21:42:12.612][biodb::testContext]
biodb.INFO [2024-10-02 21:42:12.613][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:12.614][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:12.617][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:12.618][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-02 21:42:12.618][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.621][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-02 21:42:12.622][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.624][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-02 21:42:12.625][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.627][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-02 21:42:12.628][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-02 21:42:12.628][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-02 21:42:12.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.630][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[2024-10-02 21:42:12.631][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-02 21:42:12.632][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-02 21:42:12.632][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.635][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-02 21:42:12.635][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-02 21:42:12.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.638][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-02 21:42:12.638][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-02 21:42:12.639][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-02 21:42:12.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.641][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-02 21:42:12.642][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.644][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[2024-10-02 21:42:12.644][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-02 21:42:12.645][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-02 21:42:12.646][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-02 21:42:12.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.648][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:12.649][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-02 21:42:12.649][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-02 21:42:12.650][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-02 21:42:12.651][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-02 21:42:12.651][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-02 21:42:12.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.654][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-02 21:42:12.655][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-02 21:42:12.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.657][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-02 21:42:12.658][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-02 21:42:12.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.660][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-02 21:42:12.661][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-02 21:42:12.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.663][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-02 21:42:12.664][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-02 21:42:12.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.666][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-02 21:42:12.667][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-02 21:42:12.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.669][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-02 21:42:12.670][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-02 21:42:12.674][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-10-02 21:42:12.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.676][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-02 21:42:12.677][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-02 21:42:12.678][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-02 21:42:12.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.680][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-02 21:42:12.681][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.682][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-02 21:42:12.683][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.684][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:12.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.685][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.686][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.686][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.687][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:12.688][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:12.688][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.689][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-02 21:42:12.690][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:12.690][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.691][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:12.692][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:12.693][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:12.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.695][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.696][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.697][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:12.698][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:12.699][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.699][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.700][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-02 21:42:12.701][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.702][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:12.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.703][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:12.704][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.705][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.705][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.706][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.707][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:12.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:12.708][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.709][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-02 21:42:12.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:12.710][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-02 21:42:12.711][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-02 21:42:12.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:12.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:12.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.716][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.716][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.717][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:12.718][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:12.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.719][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.720][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-02 21:42:12.721][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.721][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-02 21:42:12.722][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.723][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:12.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.729][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.730][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.731][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-02 21:42:12.731][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:12.732][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.733][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-02 21:42:12.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:12.734][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.735][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.736][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:12.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.738][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:12.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.740][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.741][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:12.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:12.742][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.742][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.743][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-02 21:42:12.744][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.745][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-02 21:42:12.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:12.747][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.748][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.750][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-02 21:42:12.750][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:12.751][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.752][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-02 21:42:12.753][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:12.754][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.754][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.755][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.756][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-02 21:42:12.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.757][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.757][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:12.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.760][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.760][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:12.761][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:12.762][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.762][self$setPropertyValue]
biodb.DEBUG[2024-10-02 21:42:12.763][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:12.764][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.787][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[2024-10-02 21:42:12.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.814][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-02 21:42:12.815][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-02 21:42:12.816][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-02 21:42:12.817][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-02 21:42:12.818][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:12.819][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-02 21:42:12.820][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:12.820][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:12.821][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-02 21:42:12.822][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-02 21:42:12.823][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:12.824][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-02 21:42:12.825][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-02 21:42:12.826][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-02 21:42:12.827][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-02 21:42:12.828][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-02 21:42:12.829][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-02 21:42:12.830][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-02 21:42:12.830][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:12.831][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-02 21:42:12.832][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-02 21:42:12.833][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-02 21:42:12.838][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-02 21:42:12.839][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-02 21:42:12.840][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-02 21:42:12.841][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-02 21:42:12.842][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-02 21:42:12.843][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-02 21:42:12.844][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-02 21:42:12.844][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-02 21:42:12.845][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-02 21:42:12.846][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-02 21:42:12.847][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-02 21:42:12.848][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-02 21:42:12.849][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-02 21:42:12.850][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-02 21:42:12.851][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-02 21:42:12.852][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-02 21:42:12.853][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-02 21:42:12.853][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-02 21:42:12.854][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-02 21:42:12.855][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-02 21:42:12.856][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-02 21:42:12.857][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-02 21:42:12.858][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-02 21:42:12.859][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-02 21:42:12.860][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-02 21:42:12.861][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-02 21:42:12.862][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-02 21:42:12.862][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-02 21:42:12.863][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-02 21:42:12.864][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-02 21:42:12.865][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-02 21:42:12.866][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-02 21:42:12.867][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-02 21:42:12.868][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-02 21:42:12.869][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-02 21:42:12.870][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-02 21:42:12.871][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-02 21:42:12.872][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-02 21:42:12.872][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-02 21:42:12.873][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-02 21:42:12.874][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-02 21:42:12.875][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-02 21:42:12.876][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-02 21:42:12.877][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-02 21:42:12.878][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:12.879][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:12.880][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-02 21:42:12.881][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-02 21:42:12.881][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-02 21:42:12.882][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-02 21:42:12.883][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-02 21:42:12.884][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-02 21:42:12.885][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-02 21:42:12.886][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-02 21:42:12.887][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-02 21:42:12.888][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-02 21:42:12.889][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-02 21:42:12.890][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-02 21:42:12.890][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-02 21:42:12.891][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-02 21:42:12.892][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-02 21:42:12.893][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-02 21:42:12.894][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-10-02 21:42:12.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-02 21:42:12.896][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.905][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[2024-10-02 21:42:12.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.909][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[2024-10-02 21:42:12.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.926][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[2024-10-02 21:42:12.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.930][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[2024-10-02 21:42:12.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.950][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[2024-10-02 21:42:12.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-02 21:42:12.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:12.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:12.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:12.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:12.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:12.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:12.971][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-02 21:42:12.972][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-02 21:42:12.973][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.974][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.975][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-02 21:42:12.976][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.977][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.978][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-02 21:42:12.978][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-02 21:42:12.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-02 21:42:12.980][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.980][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-02 21:42:12.981][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-02 21:42:12.982][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-02 21:42:12.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-02 21:42:12.983][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-02 21:42:12.983][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-02 21:42:12.984][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-02 21:42:12.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-02 21:42:12.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-02 21:42:12.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-02 21:42:12.987][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-02 21:42:12.988][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:12.988][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-02 21:42:12.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-02 21:42:12.989][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-02 21:42:12.990][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-02 21:42:12.990][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-02 21:42:12.990][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-02 21:42:12.991][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-02 21:42:12.992][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-02 21:42:12.993][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-02 21:42:12.994][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-02 21:42:12.995][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-02 21:42:12.996][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-02 21:42:12.999][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-02 21:42:12.999][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-02 21:42:13.000][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-02 21:42:13.001][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-02 21:42:13.002][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:13.003][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-02 21:42:13.003][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-02 21:42:13.004][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-02 21:42:13.005][biodb::testThat]
biodb.INFO [2024-10-02 21:42:13.006][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-10-02 21:42:13.006][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-02 21:42:13.007][biodb::testThat]
biodb.DEBUG[2024-10-02 21:42:13.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-02 21:42:13.012][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:13.013][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-02 21:42:13.014][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:13.015][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-02 21:42:13.017][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[2024-10-02 21:42:13.019][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-02 21:42:13.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-02 21:42:13.021][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-02 21:42:13.022][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-10-02 21:42:13.025][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-10-02 21:42:13.026][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-02 21:42:13.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-10-02 21:42:13.028][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-02 21:42:13.028][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-02 21:42:13.029][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-02 21:42:13.030][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-02 21:42:13.031][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-02 21:42:13.031][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-02 21:42:13.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:13.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:13.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:13.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:13.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:13.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:13.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-02 21:42:13.041][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-10-02 21:42:13.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-02 21:42:13.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-02 21:42:13.044][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-10-02 21:42:13.447][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-10-02 21:42:14.415][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-02 21:42:14.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-10-02 21:42:14.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-10-02 21:42:14.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-10-02 21:42:14.423][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-02 21:42:14.423][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-02 21:42:14.424][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-02 21:42:14.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-02 21:42:14.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:14.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:14.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:14.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:14.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:14.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-02 21:42:14.443][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.444][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.445][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.457][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:14.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:14.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.459][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-02 21:42:14.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-02 21:42:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.462][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:14.463][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:14.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.464][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-02 21:42:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-02 21:42:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.468][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-02 21:42:14.469][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-02 21:42:14.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.470][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.471][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-02 21:42:14.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-02 21:42:14.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.473][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.474][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:14.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:14.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.476][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.477][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-02 21:42:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.479][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:14.480][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:14.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.481][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.482][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-02 21:42:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-02 21:42:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:14.485][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:14.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.487][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:14.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-02 21:42:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.490][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:14.491][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:14.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.492][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-02 21:42:14.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-02 21:42:14.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.496][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:14.497][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:14.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-02 21:42:14.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-02 21:42:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.502][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:14.502][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:14.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-02 21:42:14.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-02 21:42:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-02 21:42:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-02 21:42:14.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-02 21:42:14.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-02 21:42:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-02 21:42:14.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-02 21:42:14.534][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-10-02 21:42:14.537][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-02 21:42:14.538][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-02 21:42:14.538][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-02 21:42:14.539][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-02 21:42:14.540][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-02 21:42:14.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-02 21:42:14.541][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-02 21:42:14.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-02 21:42:14.542][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-02 21:42:14.542][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
14.745 0.499 53.560
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.681 | 0.061 | 1.628 | |
| ChebiEntry | 0.105 | 0.004 | 0.109 | |